F - Genoks

Transcription

F - Genoks

CATALOG 2014 / 2015
TABLE OF CONTENTS
A
A
Microsynth – At a Glance . . . . . . . . . . . . . . . . 2
B
Quality System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
C
Ecological Commitment . . . . . . . . . . . . . . . . . 4
D
Customer Support —
We Are Here to Help . . . . . . . . . . . . . . . . . . . . . . 5
E
DNA/RNA Synthesis . . . . . . . . . . . . . . . . . . . . . . . 7
E.1
E.1.1
DNA & RNA Oligonucleotides . . . . . . . . . . . . . . . . . . . . . .
Best Price Segment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
 DNA Oligos — Large-Volume Orders . . . . . . . . . . . .
 Unmodified DNA Oligos — 1-Year Subscription Orders . . . . . . . . . . . . . . . . . . . . . .
 RNA Oligos — Large-Volume Orders . . . . . . . . . . . .
 siRNA — Large-Volume Orders . . . . . . . . . . . . . . . . . .
Standard Segment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
 Unmodified DNA Oligos . . . . . . . . . . . . . . . . . . . . . . . .
 Modified DNA Oligos . . . . . . . . . . . . . . . . . . . . . . . . . . .
 Dual-labeled Probes . . . . . . . . . . . . . . . . . . . . . . . . . . . .
 MGB and LNA Substitutes . . . . . . . . . . . . . . . . . . . . . . .
 DNA Oligos for NGS Applications . . . . . . . . . . . . . . .
 Antisense DNA Oligos . . . . . . . . . . . . . . . . . . . . . . . . . .
 Unmodified RNA Oligos . . . . . . . . . . . . . . . . . . . . . . . .
 Modified RNA Oligos . . . . . . . . . . . . . . . . . . . . . . . . . . .
 siRNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
 DNA/RNA Oligos — Click Chemistry . . . . . . . . . . . . .
 Oligos Delivered in 2D Barcoded Storage
Tubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Premium Segment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
 Unmodified DNA Oligos — Best Quality . . . . . . . . .
 Modified DNA Oligos — Best Quality . . . . . . . . . . . .
 RNA Oligos — Best Quality . . . . . . . . . . . . . . . . . . . . .
 Dual-labeled Fluorescent Probes —
Best Quality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
 Large-scale Synthesis of DNA and
RNA Oligonucleotides . . . . . . . . . . . . . . . . . . . . . . . . . .
E.1.2
E.1.3
7
7
7
8
8
8
9
9
10
12
13
13
13
14
15
16
17
17
17
18
18
19
F.2
F.2.1
DNA Sanger Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . .
Best Price Segment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
 Barcode Economy Run Service . . . . . . . . . . . . . . . . . .
 Barcode High-Throughput Service . . . . . . . . . . . . . .
 High-Throughput Service — Large-Volume Orders . . . . . . . . . . . . . . . . . . . . . . . . . . .
F.2.2 Standard Segment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
 Economy Run Service . . . . . . . . . . . . . . . . . . . . . . . . . . .
 High-Throughput Service . . . . . . . . . . . . . . . . . . . . . . .
 Ready-to-Load Sequencing . . . . . . . . . . . . . . . . . . . . .
F.2.3Premium Segment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
 Premium Run Service . . . . . . . . . . . . . . . . . . . . . . . . . . .
 Primer Walking Service . . . . . . . . . . . . . . . . . . . . . . . . .
 Large Construct Sequencing . . . . . . . . . . . . . . . . . . . .
 Clone & Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
 Exon Sequencing & Mutation Detection . . . . . . . . .
 GLP-Compliant Sequencing . . . . . . . . . . . . . . . . . . . . .
 Additional Services . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
F.3
Next Generation Sequencing . . . . . . . . . . . . . . . . . . . . . .
F.3.1Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
F.3.2Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
F.3.3 Practical Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
F.3.4 The Microsynth Advantage . . . . . . . . . . . . . . . . . . . . . . . .
F.4
Real-Time PCR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
F.4.1 Project-based Analysis Services . . . . . . . . . . . . . . . . . . . .
F.4.2 Customized and Ready-to-Use qPCR Assays . . . . . . .
F.4.3Multiplex qPCR Assays for Advanced Food
Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
F.5Genotyping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
F.5.1 Fragment Length Analysis . . . . . . . . . . . . . . . . . . . . . . . . .
F.5.2 Human Cell Line Testing . . . . . . . . . . . . . . . . . . . . . . . . . . .
22
22
23
24
25
26
26
27
27
27
28
29
29
30
30
30
31
32
32
33
34
35
36
36
36
37
38
38
39
B
C
D
E
F
G
Molecular Biology Project
Outsourcing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
G.1
G.2
G.2.1
G.2.2 G.2.3 Our Know-how for Your Success . . . . . . . . . . . . . . . . . . . .
Project Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Eradication of Bovine Virus Diarrhoe . . . . . . . . . . . . . . .
Metagenomic Analysis of Gut Microbiota . . . . . . . . . .
Detection of Cow & Pig DNA in Heparin . . . . . . . . . . . .
40
40
41
42
43
H
Terms and Conditions . . . . . . . . . . . . . . . . . . . . 44
G
19
20
F
DNA/RNA Analysis & Sequencing . . . . 21
F.1
DNA/RNA Isolation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
1
H
A
A
Microsynth – At a Glance
Microsynth AG is a private and independent life science corporation with
its headquarter in Balgach, Switzerland. With Microsynth Austria GmbH in
Vienna, Austria, and Seqlab GmbH in
Göttingen, Germany, it operates two
subsidiaries in markets where the company expects substantial growth over
the coming years.
Microsynth AG was founded by Dr.
Tobias Schmidheini in 1989 and is currently active in three different business
areas. When Dr. Schmidheini started in
1989 to produce DNA oligonucleotides
on behalf of Swiss academic institutes,
he was one of the pioneers in this area.
Meanwhile the company is offering its
numerous customers a broad spectrum
of high-quality DNA/RNA oligonucleotides (unmodified, modified, various
purification procedures etc.). In 1992
the company decided to enter the business field of DNA sequencing. Today,
the company is also well positioned in
this area being able to offer its customers both traditional Sanger sequencing services as well as state-of-the art
Front view of the Microsynth AG headquarter
in Balgach, Switzerland, where the company
owns a 3 floor building with an oligo production facility, analytic laboratories and offices of
2‘000 m2.
2
next generation sequencing services.
The third business area (molecular biology project outsourcing) is essentially a
combination of DNA/RNA synthesis with
DNA sequencing along with a couple of
other expert areas (DNA/RNA isolation,
Real-Time PCR, genotyping) where customers can rely on Microsynth’s broad
expertise and outsource entire research
projects.
Microsynth Austria GmbH was incorporated in 2012 primarily to better serve
the Austrian as well as the bordering
Eastern European markets with highquality Sanger DNA sequencing services.
Microsynth Austria is located in the heart
of Vienna where it operates modern lab
and office facilities.
Seqlab GmbH is a leading company in
the area of DNA Sanger sequencing in
the German market. Since 1996 the company is dedicated to providing all kinds
of traditional Sanger sequencing services at the highest quality to its customers from academic institutes and companies in the life science area.
Image of the industrial building at the Leberstrasse 20 in Vienna. Microsynth Austria GmbH
is housed on the 4th floor.
In early 2013 Seqlab and Microsynth decided to merge.
Bernd-Peter Ernst (CEO and co-founder of Seqlab
GmbH, left) and Tobias Schmidheini (CEO and
founder of Microsynth AG) in the lab of Seqlab
in Göttingen.
As a consequence, both companies bring
together 40 years of experience in the
area of DNA sequencing which will help
them to strengthen their position at the
forefront of this fast changing and highly
competitive market. While Seqlab will
primarily profit from Microsynth’s more
diverse portfolio of molecular biology
products and services, Microsynth will
gain better access to the German life science market.
Image of the industrial building at the Hannah-Vogt-Str. 1 in Göttingen. Seqlab GmbH is
housed on the 2nd floor where it occupies stateof-the-art lab and office facilities.
B
Quality System
Quality awareness is a prime concern
to us. This includes the quality of all Microsynth’s products and services as well
as the quality of all processes and procedures at Microsynth AG and its subsidiaries. That‘s why Microsynth’s quality management system has been ISO 9001:2008
certified, and is periodically recertified.
Moreover, parts of the analytic laboratories of Microsynth AG (DNA Sanger
sequencing and the paternity testing
laboratories), are accredited according to
the standard ISO/IEC 17025:2005 (STS),
which is a formal recognition of our competence to produce valid analytical results in a consistent manner.
As a significant part of the ISO requirements, we have extensively internalized
the process of continual improvement.
This has become a valued and vital part
of the everyday work of our employees
at all levels.
B
STS 429
DNA Sanger
Sequencing
Paternity Testing
Certification according to ISO 9001:2008
Accreditation according to EN ISO 17025:2005
3
C
C
Ecological Commitment
Microsynth and its subdiaries are committed to sustainable development1, as
illustrated in the following examples:
– Wherever possible, we sort waste materials for recycling and use the recycled products
– Microsynth AG has recently completed
the installation of a new state-of-theart photovoltaic power system at its
headquarter in Balgach, Switzerland
(see also images below). 79 solar panels covering a total area of 130 m2
produce a total annual power output
of roughly 18’000 kWh. This amount
of power is usual enough to satisfy
the need of 4–5 single family houses.
In addition, Microsynth purchases
each year 200’000 kWh eco power
(PUREPOWERgraubünden) from Rhätia Energie AG. In total, Microsynth
AG consumes electricity of approximately 280’000 kWh/year. Therefore,
78% or more than three-quarters of
Microsynth AG’s total power consumption comes from renewable energy
sources.
– Our printed materials are predominantly made from recycled fiber-based
paper or FSC-certified paper
– To visit our customers in Switzerland
and Austria, our sales forces primarily
use the train or cars from Mobility carsharing
Craftsmen at work. Solar panels were first deposited on the rooftop of Microsynth’s new building before they were installed on the angular
rooftop of the old building.
130 m2 of solar panels are ready to capture the
frequent sunlight of the St. Galler Rhine valley.
This area is known for its above average number
of sunny days within Switzerland.
In the near future, Microsynth and its
subsidiaries will attempt to achieve further improvements and optimizations to
produce and analyze as sustainably as
possible.
It is our aim to organize our processes
and work flows using a minimum of resources and waste.
We are convinced that the sustainable
way of working will be the foundation of
our economic future.
1) “Sustainable development meets the needs of the present without compromising the ability of future generations to meet their own needs. This is the most
frequently quoted definition for sustainable development. It is from “Our Common Future”, also known as the Brundtland Report.
4
D
Customer Support — We Are Here to Help
Microsynth and its subdiaries stand behind each and every product and service
offered, and take pride in offering the
highest level of customer and technical
support. We have a staff of highly-trained
molecular biologists/ biochemists as well
as administrative personnel ready to assist with any questions that you may
have. If you have any question, please do
not hesitate to call us!
Microsynth AG – Switzerland
Your contact persons for administrative questions:
Dario Semadeni, Monika Raschle and Denise Schmidheini
Phone: +41-71-722 83 33
E-Mail:[email protected]
Your contact persons for technical questions:
DNA/RNA Synthesis
Dr. Fabian Axthelm and Dr. Markus Schmid
Phone: +41-71-722 83 33
DNA/RNA Analysis & Sequencing
Sanger DNA Sequencing
Dr. Patrick Kehl, Ulrike Kuster and Katja Längle
Phone: +41-71-722 83 33
[email protected]
NextGen Sequencing & Bioinformatics
Dr. Thomas Gächter
Phone: +41-71-726 10 05
Christof Wunderlin
Phone: +41-71-726 10 01
DNA/RNA Isolation & qPCR & Genotyping
Dr. Emanuel Hörler (DNA/RNA Isolation)
Phone: +41-71-726 10 02
Dr. Vital Wohlgensinger (qPCR, Genotyping)
Phone: +41-71-726 10 50
E-Mail: [email protected]
Dr. Georges Wigger (Paternity Testing)
Phone: +41-71-726 10 08
Rainer Follador (Bioinformatics)
Phone: +41-71-726 15 51
Molecular Biology Project Outsourcing
Dr. Tobias Schmidheini
Phone: +41-71-722 83 33
Your contact persons for sales questions:
Switzerland
Dr. Christoph Grünig
Phone: +41-71-726 12 55
Germany & Austria
For Germany see under Seqlab GmbH on page 6
For Austria see under Microsynth Austria GmbH on page 6
Rest of World
Dr. Tobias Schmidheini
Phone: +41-71-722 83 33
Next Generation Sequencing
Dr. Dominique Reichert
Phone: +41-71-722 83 33
5
D
Microsynth Austria GmbH
Your contact person for administrative questions:
Bernhard Binishofer
Phone: +43-743 39 69
Technical questions will be predominantly answered by Microsynth AG in Switzerland (for corresponding business areas
and responsible persons see page 5).
Your contact person for sales questions:
Dr. Lukas Hartl
Phone: +43-699 172 460 10
Seqlab GmbH and Microsynth AG – Germany
D
Your contact person for administrative questions:
Katharina Dörnte
Phone: +49-551 370 00 10
Sanger DNA Sequencing
Dr. Karla Busch and Dr. Michael Betzler
Phone: +49-551-370 00 15 and +49-551-370 00 17
E-Mail: [email protected] and [email protected]
Technical questions for all other business areas will be predominantly answered by Microsynth AG in Switzerland
(for corresponding business areas and responsible persons see page 5).
Your contact persons for sales questions:
Dr. Barbara Siefker (Northern Germany)
Phone: +49-173 -738 40 27
[email protected]
Dr. Atila Durmus (Southern Germany)
Phone: +49-160-962 270 24
[email protected]
6
Georg Brenzel (Eastern Germany)
Phone: +49-176-649 34 562
[email protected]
E
DNA/RNA Synthesis
E.1
DNA & RNA Oligonucleotides
E.1.1 Best Price Segment
Are you looking for DNA and RNA oligonucleotides at low synthesis scales? And
are you prepared to purchase a fixed
amount of DNA/RNA oligonucleotides?
Then our Best Price Segment is right for
you.
Overall Service Features and Benefits:
•Stringent quality control: you can
expect a high level of quality since
oligonucleotides undergo a stringent
quality control (Online Trityl Monitoring during synthesis on every coupling
reaction and MALDI-TOF or analytical
PAGE)
• Technical support & consulting via
e-mail and phone: do you have questions regarding your proposed application/experiment or the experimental
outcome? Then e-mail or phone us
and we will do our best to support
you.
• Best price available: the higher the
order volume, the better price you will
be offered
•Special offer required: please first
contact us at Microsynth and request
your offer!
 DNA Oligos — Large-Volume Orders
Do you need large amounts of standard DNA oligos (>3000 DNA bases per
one single order) or large amounts of
oligos with a certain modification (e.g.
amino, FAM or 5-Met-dC modifications)?
Depending on the number of oligos or
modifications to be ordered, you will
benefit from volume-dependent discounts.
Unmodified DNA Oligos — Large-Volume Orders1
# DNA Bases
3‘000–6‘000
6‘001–12‘000
12’001–30’000
30’001–50’000
50’001–125’000
125’001– 250’000
>250’000
# of DNA
Oligos2
100–200
201–400
401–1’000
1’000–1’666
1’667–4’167
4’168–8’333
>8’333
Production
Time [weeks]
1
1–2
1–2
2
2–4
3–5
>5
Other Specifications
• synthesis scale: genomics or 0.04 µmol
• length: 13–503 bases
• guaranteed yield4: 3 OD
• purification: desalted
• QC: MALDI-TOF or PAGE
• delivery: in 96-/384-well plates or in single tubes; either dry or in solution (100 µM)
Price
per Base
Want the best
price possible?
Then please
contact us (info@
microsynth.ch)
and request your
offer!
1) Large-volume order means ≥3’000 bases or ≥100 oligos per one single order.
2) Calculation applies to unmodified oligos with 30 DNA bases.
3) For oligos >50 bases please contact us.
4) Applies to unmodified oligos >20 DNA bases
Modified DNA Oligos — Large-Volume Orders
To profit from best price possible, please contact us at Microsynth and request your offer!
7
E
J Unmodified DNA Oligos — 1-Year
Subscription Orders
In order to benefit from special conditions related to unmodified DNA oligos
at low synthesis scales (genomics and
0.04 µmol scale), in general you have to
fulfill two conditions:
1. Your annual volume/need is ≥100 oligonucleotides
2. You are prepared to purchase a certain
amount of oligos within a 1-year period
J RNA Oligos — Large-Volume Orders
Do you need large amounts of single
stranded RNA oligos (≥500 RNA bases
per one single order)? Depending on the
number of oligos you are going to order,
you will benefit from a batch-specific discount.
Procedure: You estimate your annual
need of oligos to your best knowledge 
we make you an offer  you profit from
the offered price upon your first order
 should you be significantly below or
above your estimate following 1 year, we
would make you a new proposal.
Single Stranded RNAs — Large-Volume Orders1
# RNA Bases
500–1‘250
1‘251–2’500
2’501–3’750
3’751–5’000
5’001–7’500
7’501–12’500
>12’500
E
# of RNA
Oligos2
20–50
51–100
101–150
151–200
201–300
301–500
>500
Production
Time [weeks]
1
1–2
1–2
2
2–4
3–5
>5
• synthesis scale: genomics or 0.04 µmol
• length: up to 25 bases
• guaranteed yield: 2 OD
• average yield: 4 OD
• QC: MALDI-TOF
• delivery: dried, in single tubes or plates
Price
per Base
Want the best
price possible?
Then please
contact us (info@
microsynth.ch)
and request your
offer!
1) Large-volume order means ≥500 bases or ≥20 oligos per one single order.
2) Calculation applies to RNA oligos with 25 RNA bases
J siRNA — Large-Volume Orders
Do you need large amounts of siRNAs
(≥12 siRNA Duplexes per one single
order)? Depending on the number of
siRNAs you are going to order, you will
benefit from a batch-specific discount.
siRNAs — Large-Volume Orders1
# siRNAs
12–30
31–60
61–100
101–200
201–300
>300
Production
Time [weeks]
2
2–3
2–3
3
3–5
>6
• synthesis scale: 0.04 µmol
• length: 2 x 21 bases
• guaranteed yield: 2 OD
• average yield: 4 OD
• QC: MALDI-TOF
• delivery: in solution (40 µM, already annealed and ready to
use)
1) Large-volume order means ≥12 siRNAs per one single order.
8
Price
per siRNA
Want the best
price possible?
Then please
contact us (info@
microsynth.ch)
and request your
offer!
E.1.2 Standard Segment
Are you looking for a broad spectrum of
DNA and RNA oligonucleotides which
can be subjected to various modification and purification procedures and in
addition can be ordered at various synthesis scales? Then our Standard Segment is right for you.
 Unmodified DNA Oligos
We use state-of-the art synthesizer technologies and purification methods to
•Broad range of synthesis scales,
modifications and purification procedures
• Stringent quality control: you can
expect a high level of quality since
oligonucleotides undergo a stringent
quality control (Online Trityl Monitoring during synthesis on every coupling
PAGE)
•Extended Certificate of Analysis (ExCoA): different types of ExCoA’s available
•Technical support & consulting via
e-mail and phone: do you have questions regarding your proposed application/experiment or the experimental outcome? Then e-mail or phone
us and we will do our best to support
you.
• No minimum order volume
offer you unmodified DNA oligos with
4 different purity levels:
Desalted Oligos
Synthesis
Scale1
Genomics
0.04 µmol
0.2 µmol
1.0 µmol
15 µmol
Length
[Bases]
13–39
13–80
6–1504
6–80
13–60
Guaranteed Yield
[OD260]2
[nmol]3
2
10
3
15
10
50
50
250
700
3‘500
Average Yield
[OD260]2
8
9
20
80
1’000
Length
[Bases]
Guaranteed Yield
[OD260]2
[nmol]3
13–50
6–50
6–50
6–50
1
3
15
300
Average Yield
[OD260]2
not available
4
7
26
500
[nmol]3
40
45
100
400
5’000
Production
Time [wd]
1
1
1
1
2
[nmol]3
Production
Time [wd]
20
35
130
2‘500
2
2
2
3
[nmol]3
Production
Time [wd]
30
100
2‘000
3
3
4
HPLC Purified Oligos
Synthesis
Scale1
Genomics
0.04 µmol
0.2 µmol
1.0 µmol
15 µmol
5
15
75
1‘500
HPLC Purified & Dialysed Oligos
Synthesis
Scale1
Genomics
0.04 µmol
0.2 µmol
1.0 µmol
15 µmol
Length
[Bases]
Guaranteed Yield
[OD260]2
[nmol]3
8–50
8–50
8–50
3
15
200
15
75
1‘000
Average Yield
[OD260]2
not available
not available
6
20
400
9
E
PAGE Purified Oligos
Synthesis
Scale1
Genomics
0.04 µmol
0.2 µmol
1.0 µmol
15 µmol
Length
[Bases]
Guaranteed Yield
[OD260]2
[nmol]3
13–80
8–1504
8–80
0.5
1
7
2.5
5
35
Average Yield
[OD260]2
not available
6
8
20
[nmol]3
Production
Time [wd]
30
40
100
2
2
2
not available
1) The synthesis scale represents the initial amount of 3‘ bases (starting material).
2) Guaranteed and average yields in OD are valid for unmodified oligos >20mer only.
3) Yields indicated in nmol represent an example calculation for a 20mer. For this calculation the following rule of thumb equation was applied: nmol of oligo = OD x
100/length of oligo. Please note that this calculation is based on sequences with virtually homogenous distribution of the 4 DNA bases; it may vary for sequences
with high GC contents >70% etc.
4) Oligos longer than 150 DNA bases on request (we would like to discuss the proposed experiment/application with you beforehand in order to guarantee the
best possible outcome)
J Modified DNA Oligos
Microsynth offers a wide variety of modifications (5’, 3’ and internal) for DNA oligonucleotides. The following 3 tables
represent the most common modifications our customers are usually asking
for. If your desired modification is not
listed here, please contact us for availability.
Modifications involving the DNA Base and/or Sugar-phosphate Backbone
E
Type of Modification
Amino-dT*
Azido-dT*
2-Aminopurine
Biotin-dT
5-Br-dC and 5-Br-dU*
2’-Deoxyinosine (INO)
2’-Deoxyuridine (dU)
3’-Deoxy-dA, dC, dG and dT1
5-Met-dC
5-OH-Met-dC*
N6-Met-dA*
Mixed Bases
Phosphorothioate bases (PTO)
Spacer C18 (HEG)
Spacer C3
Spacer C12
dSpacer (abasic site)
TIPS-Alkyne-(C8)-dT*
TMS-Alkyne-(C8)-dT*
* Price on request
Position
5’
3’
x
x
x
x
x
x
1) 3’-Deoxy-dA, dC, dG and dT is equivalent to 2’3’ Dideoxy A/G/C/T
10
Int.
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
Synthesis Scale [µmol]
0.04
0.2
1.0
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
Purification
Des
HPLC
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
PAGE
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
Non-Fluorescent Modifications
Position
Synthesis Scale [µmol]1Purification
5’
3’
Int.
0.04
0.2
1.0
Des
HPLC
PAGE
Alkyne (Click Chemistry) x xxxxx
Aminolink (C6) x xxxxxx
Aminolink (C6 or C7)2 x xxxxx
Biotin (C6) x
x
x
x
x
x
Azide (Click Chemistry) x
x
x
x
x
x xx xxx
Biotin (TEG)
x
x
x
x
x
Cholesterol
x
x
x
x
Digoxigenin
xx xx xx
DBCO (Cu-free Click Chemistry) x
x
x
x
x
x
Hexynyl (Click Chemistry)
x
x
x
x
x
x
Inverted Thymidine x xxxxx
Phosphorylation
x xxxxxx
x xxxxx
Thiol (C6)
x
x
x
x
x
Thiol (C3)
x
x
x
x
x
Other modifications on request
1) 15 µmol scale available on request
2) 3‘ Aminolink C7 is used for oligos >50 bases
Fluorescent or Dye Modifications
Position
Synthesis Scale [µmol]1Purification
5’
3’
Int.
0.04
0.2
1.0
Des
HPLC
PAGE
AlexaFluor 350/430
xx xx xx
ATTO 425/532/550/565/590/620/
x xxx xx
647N x xx xx
BHQ-1/BHQ-2
x
x
x
x
x
Cy3/5/5.5/Cy7
x xxx xx
x xx xx
Dabcyl
x
x
x
x
x
Dyomics 510XL/530/630/681 x xxx xx
x
x
x
x
x
Dyomics 781
x
x
x
x
x
x
x
x
x
FAM
x xxx xx
x
x
x
x
HEX
x xxx xx
Joe
xx xx xx
Rox
xx xx xx
TAMRA
xx xx xx
TET
x xxx xx
Texas Red
x
x
x
x
x
Yakima Yellow
x
x
x
x
x
Other modifications on request
1) 15 µmol scale available on request
11
E
J Dual-labeled Probes
Microsynth offers a wide selection of
fluorophores and quenchers which will
support most real-time quantitative PCR
instruments and multiplex analysis systems. Here are some arguments to use
dual-labeled probes, especially those
from Microsynth.
Main Product Features and Benefits:
• Broad portfolio of probes: availability
of various fluorophore and quencher
combinations
• High quality: all probes are MALDITOF controlled before shipment
• Minimum delivery guarantee (delivered amount is on average at least 3
times higher)
• Fast delivery (within 3 working days
on average)
• Competitive and transparent pricing: prices for dual-labeled probes
include all DNA bases, fluorophores &
quenchers as well as a thorough purification procedure (HPLC or even PAGE)
• Free of charge: free probe design service available; design of dual-labeled
probes and primer pairs on request
• Additional services
– Design, synthesis and functionality
testing of primer-probe sets for realtime PCR
– C-5 propynyl modification of your
probe (as alternatives for MGB and
LNA probes)
– Aliquotation of probes and shipment
within 5 tubes on request
– If your qPCR experiment requires
the use of FRET hybridization probes
(probes for LightCycler®) or Molecular Beacons, Microsynth can of
course help you with respect to design and synthesis of high-quality
primer-probe sets.
Fluorophores and Quenchers
5‘ Label
3‘ Label
TAMRA
1.0 µmol Scale1
Minimum
Average
Yield2
Yield2
10 OD
30 OD
50 nmol
150 nmol
8 OD
25 OD
40 nmol
125 nmol
10 OD
30 OD
5 nmol
150 nmol
3 OD
15 nmol
TAMRA
n/a
n/a
Dabcyl
n/a
n/a
2 OD
10 nmol
5 OD
25 nmol
10 OD
50 nmol
20 OD
100 nmol
BHQ-1
n/a
n/a
1.5 OD
7.5 nmol
6 OD
30 nmol
8 OD
40 nmol
25 OD
125 nmol
BHQ-1
E
0.2 µmol Scale1
Minimum
Average
Yield2
Yield2
8 OD
2 OD
40 nmol
10 nmol
9 OD
45 nmol
2 OD
8 OD
10 nmol
40 nmol
1 OD
5 nmol
FAM
HEX
TET
AlexaFluor 350
FAM
HEX
TET
AlexaFluor 350
HEX
JOE
TET
ATTO 425/532
Yakima Yellow
0.04 µmol Scale1
Minimum
Average
Yield2
Yield2
(equivalent to VIC)
ATTO 647N
ATTO 620
ATTO 550
(equivalent to NED)
1.5 OD
4 OD
8 OD
Cy3/Cy5
BHQ-2
n/a
n/a
7.5 nmol
20 nmol
40 nmol
Dyomics 681
ROX
TAMRA
Texas Red
If your desired fluorophore or quencher is not listed in this table, please contact us for availability and pricing.
15 OD
75 nmol
2) Yields indicated in OD260 apply to a probe consisting of 20 DNA bases; Calculation: 1 OD = 5 nmol (please note that this calculation is based on sequences with
virtually homogenous distribution of the 4 DNA bases; it may vary for sequences with high GC contents >70% etc.)
12
 MGB and LNA Substitutes
Interested in replacing your MGBTM or
LNATM probes? The MGBTM (minor groove
binding) and LNATM (locked nucleic acid)
technologies are used to enhance the
affinity of a standard oligonucleotide sequence to its complementary nucleotide
strand. Since both technologies are pat-
 DNA Oligos for NGS Applications
Do you need NGS adaptors, fusion primers or any other specific primers for your
next generation sequencing project?
Due to its vast experience in the area of
 Antisense DNA Oligos
Oligonucleotides to be used in antisense
experiments must be modified to increase their resistance against nucleases.
There are several possibilities to stabilize
oligos and to avoid enzymatic degradation during in vitro or in vivo applications.
Microsynth can offer you the following
two modifications:
ent protected, its use, distribution as well
as pricing are selectively controlled. To
overcome this disadvantage, Microsynth
has established a cost-effective alternative to enhance the affinity properties
of normal DNA/RNA oligonucleotide sequences. Microsynth offers four different
modifiers that can be used as substitutes
for the normal bases C, U, and A during
synthesis. Interested in receiving more
information? Then please visit our website or contact us ([email protected]).
oligonucleotide synthesis as well as next
generation sequencing, Microsynth will
be your partner of choice.
In order to receive more information or
to get a tailor-made offer, please contact
us ([email protected]).
•PTO (phosphorothioates) modifications: PTOs contain one sulfur atom in
place of an oxygen atom in the internucleotide linkage of DNA or RNA. This
modification of the normal phosphodiester backbone is characterized by an
increased cell uptake, high nuclease
resistance and elicitation of RNAse H
activity.
•2‘-O-Me-RNA modifications: The incorporation of 2‘-O-Me-RNA nucleotides induces a resistance to a wide variety of ribo- and deoxyribonucleases.
This enables the formation of more stable hybrids with complementary RNA
strands than would be the case for nonmodified DNA and RNA sequences.
Position
Synthesis Scale [µmol]1
Purification2
Modifications
5’
3’
Int.
0.04
0.2
1.0
15
HPLC + Dialysis
PTO xxxxxx
2’-O-Me-RNA
xxx xxxx
1) We strongly recommend selecting HPLC followed by dialysis as purification in order to achieve physiological condition.
2) The same guaranteed yields apply as for unmodified oligos (see also under DNA Oligos in the Standard Price Segment).
13
E
J Unmodified RNA Oligos
We utilize state-of-the art synthesizer
and chemistry technologies in combina-
tion with various purification methods to
offer you unmodified RNA oligonucleo-
tides with 4 different purity levels:
Desalted Oligos
Synthesis
Scale1
Genomics
0.04 µmol
0.2 µmol
1.0 µmol
15 µmol
Length
[Bases]
Guaranteed Yield
[OD260]2
[nmol]3
10–30
5–504
5–504
15–40
4
8
18
400
21
35
80
1‘800
Average Yield
[OD260]2
not available
6
10
22
800
[nmol]3
Production
Time [wd]
28
45
100
2‘200
2
2
2
3
[nmol]3
Production
Time [wd]
10
25
85
1‘800
2
2
2
4
[nmol]3
Production
Time [wd]
15
55
1‘250
4
4
4
[nmol]3
Production
Time [wd]3
5
35
2
2
HPLC Purified Oligos
Synthesis
Scale1
Genomics
0.04 µmol
0.2 µmol
1.0 µmol
15 µmol
Length
[Bases]
Guaranteed Yield
[OD260]2
[nmol]3
10–30
5–50
5–50
15–40
1
3
13
300
5
15
65
1‘500
Average Yield
[OD260]2
not available
2
5
17
360
HPLC Purified & Dialysed Oligos
E
Synthesis
Scale1
Genomics
0.04 µmol
0.2 µmol
1.0 µmol
15 µmol
Length
[Bases]
Guaranteed Yield
[OD260]2
[nmol]3
8–50
8–50
15–40
2
9
200
10
45
1‘000
Average Yield
[OD260]2
not available
not available
3
11
250
PAGE Purified Oligos
Synthesis
Scale1
Genomics
0.04 µmol
0.2 µmol
1.0 µmol
15 µmol
Length
[Bases]
Guaranteed Yield
[OD260]2
[nmol]3
8–504
8–504
1
6
5
30
Average Yield
[OD260]2
not available
not available
1
7
not available
2) Guaranteed and average yields in OD are valid for unmodified oligos >20 and <40 nucleotides only.
3) Yields indicated in nmol represent an example calculation for a 20mer. For this calculation the following rule of thumb equation was applied: nmol of oligo =
OD x 100/length of oligo. Please note that this calculation is based on sequences with virtually homogenous distribution of the 4 RNA bases.
4) Oligos longer than 50 RNA bases on request (we would like to discuss with you the proposed experiment/application beforehand in order to guarantee the best
possible outcome).
14
Important – Please Note!
Chimeric oligonucleotides: Chimeric
oligos (containing DNA, RNA, 2‘-O-Me-
RNA) can be easily ordered via our webshop (an additional hybrid molecule
charge will apply).
 Modified RNA Oligos
Microsynth offers a wide variety of modifications (5’, 3’ and internal) for RNA oli-
gonucleotides. If your desired modification is not listed in the following tables,
please contact us for availability.
Modifications involving the RNA Base and/or Sugar-phosphate Backbone
Position
Purification
5’
3’
Int.
0.04
0.2
1.0
DES
HPLC
PAGE
2’-O-Methyl-RNA
xxx xxxxx
PTO x xxxxx
2’-Fluor-RNA
x x xxxxx
Non-Fluorescent Modifications
Position
Purification
5’
3’
Int.
0.04
0.2
1.0
DES
HPLC
PAGE
Aminolink (C6)
x xx xx
Aminolink (C6) x xx xx
Biotin (C6)
x xx xx
Biotin (TEG) x xx xx
Cholesterol x xxx x
Digoxigenin
xx xx xx
Inverted Thymidine x xxxxx
Phosphorylation
xx xxxxx
Spacer C3 xx xxxxx
Thiol
xx xxxxx
4-Thio-rU* x x xxxxx
* Price on request
Fluorescent or Dye Modifications
Position
Purification
Modifications
5’ 3’ Int.0.04
0.21.0DESHPLC
PAGE
Cy3/Cy5/Cy 5.5/Cy7
xx xx xx
Dyomics 681
xx xx xx
Dyomics 781
xx xx x
FAM
xx xx xx
TAMRA
xx xx xx
BHQ 1/BHQ 2 x xx xx
15
E
J siRNA
siRNA, or small interfering ribonucleic
acid, is a type of RNA that is involved in
a number of biological processes, most
notably RNA interference. RNA interference is a regulatory process that is used
to control and limit the expression of
specific genes. While most RNA is single
stranded, siRNA is made up of two complementary strands of RNA nucleotides
similar to those in DNA. Usually siRNA
molecules are 21-23 nucleotide doublestranded RNA (dsRNA) duplexes with
symmetric 2-3 nucleotide 3’ overhangs.
Main Product Features and Benefits
• High quality: all siRNAs are MALDI-TOF
controlled before shipment
• Guaranteed yields: high quantity delivered (actual delivered amount significantly higher than minimal guaranteed yield)
Synthesis Scale1
0.04 µmol
0.2 µmol
E
• Ready to use: fully deprotected,
siRNAs already annealed and ready to
use (40 µM)
• Fast delivery:
– Shipment within 24 hours (valid
only for single orders; orders must
be placed before 10 AM, and a short
note should reach us by telephone)
– Shipment within 48 hours (valid
only for single orders; for volume orders please request information on
delivery time)
• Free of charge: free siRNA design service available
• siRNA Design Tool: by using our online siRNA design tool you can design
your siRNAs on your own (our design
tool represents a customized tool that
combines published design criteria
with valuable experiences made by Microsynth). To use our siRNA design tool,
Desalted
OD2602
9
16
[nmol]2
21
35
HPLC
OD2602
4
7
please login first to our webshop and
choose siRNA > siRNA Design Tool.
• Additional services:
– Modified siRNAs are available on request
– Guaranteed knock down: if you use
our free siRNA design service and let
us produce ≥ 3 siRNAs, we guarantee
that at least one of the synthesized
siRNAs will reduce mRNA levels by at
least 70%1
Microsynth supplies classical siRNA duplexes (2x21-mers) and longer duplexes
up to 27-mers with 3 different levels of
purity (see table below):
[nmol]2
8
16
PAGE
[OD260]2
[nmol]2
not available
2
5
Classical siRNA duplexes (2x21-mers) have unit prices; if you need longer duplexes, each additional RNA base will be priced accordingly. Modified siRNAs are
available upon request (please see the section “RNA Oligos – Modified” for the range of modifications Microsynth offers as a standard service).
2) Yields indicated represent guaranteed yields and apply to a 2x21mer; Calculation: 1 OD = ~2.5 nmol (please note that this calculation is based on sequences with
virtually homogenous distribution of the 4 RNA bases)
Microsynth supplies the following two
types of control siRNAs:
• Pre-synthesized Control siRNAs
• Scrambled siRNAs (Customized Negative Control siRNA)
1) Conditions:
Service is limited to 5 genes per customer and day. If you do not achieve the guaranteed 70% knock down, we design/synthesize additional 3 siRNAs for you.
However, you need to show us that your experiment was performed according to the following parameters:
– Delivery efficiency of siRNA: >90%
– Effective concentration applied: 100 nM
– Incubation: at least 48 hours
– Positive control: included
16
 DNA/RNA Oligos — Click Chemistry
Click chemistry is a new versatile approach that can be used for the synthesis of a great variety of (complex) biomolecules1,2. In short, click chemistry is
a chemical reaction between an alkyne
and an azide moiety to yield a triazol
conjugate that connects two different
biochemical species (e.g. an oligonucleotide sequence with a fluorescent dye)3,4.
Due to the nature of the bond chemistry
(strong thermodynamic reaction in water, no side reactions, lack of functional
group interference etc.) this new type of
chemistry is perfectly suited to label DNA
and RNA oligonucleotides. In combination with state-of-the art nucleic acid
labeling technologies (NHS-ester and
phosphoramitide chemistry), it is now
possible to label or tag DNA and RNA at
any position. Whether you as customer
need multiple modifications with differ-
 Oligos Delivered in 2D Barcoded
Storage Tubes
Whether you need to securely store and
keep track of hundreds or thousands of
oligos, Microsynth can deliver the requested oligos in 2D barcoded storage
tubes.
ent labels within the DNA/RNA strand
(internal modifications) and/or the
termini (5’ and 3’ modifications), clickchemistry will make it feasible. Hence
click chemistry has opened a door to an
entire new world of so far unimaginable
biomolecules.
To date, click chemistry is usually applied
for the synthesis of more complex DNA/
RNA oligonucleotides. The complexity is
even more increased since click chemistry distinguishes between a coppercatalyzed ligation of azides and alkynes
and a copper-free ligation5,6. The latter
has been developed to allow the use of
DNA/RNA oligonucleotides under physiological conditions (copper is difficult
to remove or purify; residual copper is
highly toxic for bacterial as well as mammalian cells). Therefore, we would like
to invite you to send us your request
([email protected]) by indicating your
sequence & modifications demands as
well as your foreseen application. Microsynth would then check your inquiry
and come back to you with a customized
quote suggesting you a reasonable and
cost-effective synthesis approach for the
desired biomolecule.
References:
1. El-Sagheer AH, Brown T. Chem. Soc. Rev.
Chem. Soc. Rev., 2010, 39, 1388–1405.
2. V.V. Rostovtsev, Green, L.G., Fokin, V.V. and
Sharpless, K.B., Angew. Chem. Int. Ed, 2002,
41, 2596–2599.
3 R. Huisgen, Angew. Chem. Int. Ed., 1963, 2,
565–598.
4. Y.H. Zhang, et al., Tetrahedron, 2007, 63,
6813–6821.
5. I.S. Marks, et al., Bioconjugate Chemistry,
2011, 22, 1259–1263.
6. Becer CR, Hoogenboom R, and Schubert US,
Angew. Chem. Int. Ed. 2009, 48, 2–11.
Your Overall Benefits Include:
•Delivery of oligos in tubes carrying a
unique and permanently attached,
laser-etched 2D barcode at the bottom
of each tube
•
Delivery of unique data (e.g. oligo
name, sequence, yield, etc.) associated
with each tube as electronic file (*.txt;
*.csv)
•All together this results in simplified
and more secure storage, identification
as well as tracking of your oligos samples in your lab
documentation and support? Then our
Premium Segment is right for you.
•Total quality control: you can expect
the highest level of quality since all
oligonucleotides undergo a total quality control (Online Trityl Monitoring
during synthesis on every coupling
PAGE).
• Quality guarantee: we are so confident about our quality that we offer a
100% quality guarantee: If you show
us that any delivered oligo does not
meet its specification, it will be re-syn-
E.1.3 Premium Segment
Microsynth is a pioneer in the area of
oligonucleotide synthesis and can look
back on 25 years of experience. This
valuable know-how is especially leveraged when used in combination with
the latest generation of DNA synthesizer
technology as well as with high-quality
chemicals. It consequently results in oligonucleotides of the highest quality.
Are you looking for DNA or RNA oligonucleotides with the highest possible
quality including the highest level of
•Premium quality: all oligonucleotides
are subjected to our highest level of
purification (proprietary HPLC or PAGE
purification with the possibility for additional special treatment to minimize
the levels of disruptive dye blobs and
extrinsic DNA).
17
E
E
thesized free of charge at your earliest
convenience.
• Fixed delivery amounts (on request)
• Extended Certificate of Analysis
(ExCoA) available and/or customized documentation
e-mail and phone: do you have questions regarding your proposed application/experiment or the experimental outcome? Then e-mail or phone
you.
• Limited R&D included: issue-solving
involving all divisions (i.e. DNA Sequencing, Real-Time PCR, Genotyping
etc.)
• Special offer required: please first
contact us at Microsynth and request
your offer!
Important – Please note!
A standard Quality Certificate does not
meet your requirements? Then we can
offer you an Extended Certificate of Analysis as the next higher level of documentation. An extended CoA contains the
following information:
• Identity Test by means of MALDI-TOF
including the spectrum
• Purity Test by means of analytical HPLC
including the chromatogram (if secondary structure is too strong, we do
not perform this analysis)
• Purity Test by means of analytical PAGE
• Appearance Test by means of visual inspection
• Solubility Test by means of solubilization in buffer prior to lyophilization
• Information about re-suspension of
your oligo and the stability/shelf life at
different storage conditions
• Proof checked and signed by our head
of oligonucleotide production or the
delegated representative
a proprietary PAGE purification and
protocol to yield products that are, on
average, 98% pure)
• Special treatment of all disposable
materials in direct contact with the
oligonucleotide to be synthesized
• Guaranteed quantity delivered: you
can choose from 20, 40, 100, or 400
nmol amounts
• Extended Certificate of Analysis available upon request
Potential Applications:
• Gene expression profiling
• MLPA (Multiplex ligation-dependent
probe amplification)
• TRFLP (Terminal restriction fragment
length polymorphism)
• within diagnostics kits to be used for
fragment analysis of plant or animals
• Microsatellite analysis
• AFLP analysis (amplified fragment
length polymorphisms)
• Mutation detection
J Unmodified DNA Oligos —
Best Quality
According to your demand or specific
application we can produce premium
oligonucleotides meeting the highest
requirements. On a routine basis we offer
premium oligonucleotides with the following characteristics:
• All oligos are subjected to a proprietary HPLC system and protocol to
yield products that are, on average,
92% pure (On request we offer also
J Modified DNA Oligos — Best Quality
According to your demand or specific application we can produce your premium
oligonucleotides meeting the highest
premium oligonucleotides at 3 slightly
different purity levels with the following
characteristics:
Purity level 1: Proprietary PAGE
All oligos produced are subjected to a
proprietary PAGE system and protocol
to yield products that are, on average,
98% pure.
18
Purity level 2: Proprietary PAGE &
NAP
98% pure. A final desalting step by
means of NAP treatment supports the
further removal of disruptive dye blobs.
Potential Applications
• Our non-modified premium oligonucleotides are recommended for all sensitive PCR and qPCR applications, especially for diagnostic purposes.
Purity level 3: Proprietary PAGE &
NAP combined with Aseptic Handling
98% pure. A final desalting step by
means of NAP treatment supports the
further removal of disruptive dye blobs.
In order to minimize contamination of
the synthesized oligos with extrinsic
DNA traces, Microsynth has implemented following set of critical measures:
•Special treatment of all disposables in
direct contact with the oligonucleotide
to be synthesized
•Special cleaning procedure for production devices
• Dedicated production areas and SOPs
•Within diagnostics kits to be used for
human fragment analysis (e.g. forensic
applications)
•
Microsatellite analysis (human samples)
•
AFLP analysis (amplified fragment
length polymorphisms) (human samples)
• Mutation detection (human samples)
•MSI analysis (microsatellite instability
analysis) (human samples)
Spectrum of Available 5’ Labels and Guaranteed Delivery Amounts
Guaranteed Quantity Delivered [nmol]
Type of 5’ Label
20
100
400
Documentation1
FAM
xxxExCoA
JOE/Yakima Yellow
xxxExCoA
TAMRA
xxxExCoA
ROX
xxxExCoA
ATTO 425/532/550/565/620/647N
xxxExCoA
Dyomics 510XL/530/630/681/781
xxxExCoA
1) Extended Certificate of Analysis will be provided on request.
Additional Service Feature
Purification Service: Microsynth’s proprietary PAGE purification system and
protocol has an excellent reputation in
its field. For instance, many customers
send us their VICTM, NEDTM, PETTM labeled
oligonucleotides for additional purifi-
 RNA Oligos — Best Quality
If our RNA related products and services
within the Best Price or Standard Segment do not satisfy your overall needs,
 Dual-labeled Fluorescent Probes —
Best Quality
According to your demand or specific
application we can produce dual-labeled
fluorescent probes meeting the highest
dual-labeled fluorescent probes with the
following characteristics:.
•Broad portfolio of probes: availability
of various fluorophore and quencher
combinations (see also the section
cation. Please note that due to patent
issues, Microsynth may not be allowed
to tag your desired premium oligo with
any dye available on the market. However, in most cases we are able to suggest an equivalent alternative dye to fit
your needs. Therefore, please contact us
when you are looking for a cost-effective
generic dye or when you are just looking
for the best purification procedure available on the market.
then do not hesitate to contact us (info@
microsynth.ch). We are happy to discuss
your experimental outline and eventually find a good solution for you.
“Fluorophores and Quenchers” under
Related Links)
•High quality: all probes undergo a
thorough purification procedure (HPLC
or even PAGE) to yield highly pure and
functional products; prior to shipment
all probes are MALDI-TOF controlled.
• Guaranteed quantity delivered: you
can choose from 20, 100, or 400 nmol
amounts
• Professional probe design service included
•Many additional services on request:
–Enhanced hybridization (MGB or LNA
like treatment of your probe)
–
Extended Certificate of Analysis
available
–
From assay development to outsourcing of your entire Real-Time
19
E
PCR project, everything is imaginable!
J Large-scale Synthesis of DNA and
RNA Oligonucleotides
When your work requires more than nanomole quantities, Microsynth’s production facilities can accommodate largescale oligonucleotide synthesis orders
ranging from milligrams to tens of grams.
Simply scaling up conventional smallscale solid-phase oligonucleotide synthesis would be inefficient and wasteful,
requiring huge volumes and amounts
of expensive solvents and reagents. Instead, we use specialized equipment and
techniques for synthesis, purification and
quality control of bulk amounts of oligos
in order to match the demanding and
specific needs of our customers.
E
20
– Our premium dual-labeled fluorescent probes are recommended for all
sensitive PCR and qPCR applications,
especially for diagnostic purposes.
– Scalable synthesis range: mg to gram
quantities can be realized; in case
of larger projects up-scaling to kg
range is feasible.
– Oligo length: sequences up to
80mers possible
– Broad range of modifications available (e.g. Phosphorylation, Phosphorothioate, 2’-O-methyl-RNA, NH2,
FAM, Biotin, and others)
– High purity: delivery of your oligo
fully deprotected and desalted; stringent purification by HPLC available.
– Stringent quality control: your oligo
is verified using MALDI-TOF and/or
PAGE
– Additional services on request: Dialysis, Sterilization/Filtration, and Endotoxin testing
Potential Application
– Biophysical experiments such as xray crystallography
– NMR studies
– Antisense experiments in animals
– Manufacture of diagnostic kits
F
F.1
DNA/RNA Isolation
The quality and purity of the isolated
DNA or RNA has a significant impact on
the outcome of all down-stream analyses.
Therefore, it is of paramount importance
to rely on an optimized and well-proven
isolation system when starting an experiment or project with a specific DNA/RNA
source.
Microsynth looks back on more than 13
years of experience in DNA/RNA isolation
from different and difficult tissues/matrices like plant material, food or stool. Our
know-how in this area may help you to
DNA/RNA Source
Animal Tissues & Cells
Biofilm
Blood
Fecal
Food
Microbes
Plant
Soil
Water
Interested in receiving more information
or obtaining a quote? Then please do not
improve your overall productivity by allowing you to spend more time evolving
your experiments and analyzing your
data rather than expending time and effort on optimizing your DNA/RNA isolation approach.
A well-proven process for nucleic acid
isolation ensures that the following 4
steps are professionally handled:
1.
Effective disruption of the cellular
structure to generate a lysate
2.Clean separation of the soluble nucleic acids from cell debris and other
insoluble materials
3.Separation of nucleic acids from soluble proteins
4.Final high-level purification of nucleic
acids
The following table gives you an overview about the various matrices where
we have solid experience in isolating
DNA, RNA or plasmid DNA. We are also
able to develop high-throughput isolation protocols for our customers due to
our knowledge in laboratory automation.
DNA/RNA Isolation Service
DNA
RNA
Plasmid
yes
yes
n.a.
yesyesn.a.
yesyesn.a.
yesyesn.a.
yesyesn.a.
yesyesyes
yesyesn.a.
yesyesn.a.
yesyesn.a.
hesitate to contact Dr. Emanuel Hörler
([email protected]).
21
F
F.2
DNA Sanger Sequencing
Microsynth and Seqlab have many
years experience (40 years accumu-
lated) in the area of DNA Sanger sequencing. The following table gives an
overview about the various services
which we are currently offering.
Name
Description
Standard Sequencing in 1.5 ml Single Tubes
Barcode Economy Run Service
Pre-paid service; generic samples;
one tube = one reaction
Economy Run Service
Generic samples ; one tube = one reaction
Premium Run Service
Difficult samples ; one tube = one or several
reactions
Standard Sequencing within MTP (Microtiter Plate) Format
Barcode High-Throughput Service
Pre-paid service; 96-well plate format
High-Throughput Service
96- and 384-well plate format
Ready-to-Load High-Throughput
Service
Other Sequencing Services
Primer Walking Service
Large Construct Sequencing
Clone & Sequence
Exon Sequencing and Mutation
Detection
GLP-Compliant Sequencing
Post-BigDye cleanup samples;
96- and 384-well plate format
De novo as well as verification sequencing
(single- or double stranded)
Partial and entire sequencing of BACs, PACs,
FOSMIDs and COSMIDs
Partial sequencing of genomic DNA (up to 5MB)
Cloning of PCR products into a vector
and subsequent sequencing
Identification of (point) mutations in genes or
exons with great accuracy on a nucleotide level
High-quality double strand sequencing compliant
with Good Laboratory Practice (GLP)
Service Segmentation
Best Price Segment
Standard Segment
Premium Segment
Best Price Segment
Best Price Segment &
Standard Segment1
Best Price Segment &
Standard Segment1
Premium Segment
Premium Segment
Premium Segment
Premium Segment
Premium Segment
1) Upon ordering a certain volume of reactions, list prices will drop significantly; whereas Best Price Segment means high order volumes, Standard Segment means
low order volumes.
F
F.2.1
Best Price Segment
Are you looking for an experienced
Sanger DNA sequencing service that is
capable of sequencing routine samples
such as plasmids or PCR products? And
are you prepared to commit to a certain
number of reactions (e.g. for single sequencing reactions in tubes or for highthroughput sequencing reactions in
96-well plates)? Then our Best Price Segment is right for you.
22
expect a high level of quality since all
your sequencing reactions are monitored very closely for signal strength,
length of read and quality values.
e-mail and phone: do you have questions regarding your proposed application/experiment or the experimen-
tal outcome? Then e-mail or phone
you.
• Best price available: the higher the
order volume, the better price you will
be offered.
 Barcode Economy Run Service
Do you have a relatively high need for
sequencing of routine samples such

as PCR products or plasmids? Then we
recommend our Barcode Economy Run
Service.
Main Service Features and Benefits:
•Read length per run: up to 1100 bases
•Standard primers and specific primers
will be added free of charge
•Failed reactions will be repeated on request free of charge
• Convenient service
–
Easy ordering and overnight inhouse production of specific sequencing primers
–Pre-paid barcode labels can be purchased in batches of 50, 100, 250 and
500, or 1000. They have no expiration
date and can be used by multiple researchers.
–Each of our green barcode labels allows unambiguous sample identification
•
User-friendly and cost-free sample
shipment: Just use either the Microsynth/Seqlab pick-up service or request our pre-paid and pre-addressed
envelopes for cost-free shipment via
post mail (not available for all countries, just ask us for availability).
•
Rapid turnaround time: sequencing
time in the laboratory <24h
•
Direct access to support by experienced academic staff (no waiting on a
recorded-message hotline)
•Additional services:
–PCR purification available (additional
fee is applicable)
–Specific treatment for GC-rich samples (free of charge!)
Sample Requirements
General Information
DNA samples and sequencing primers can be sent pre-mixed (within one
tube) or separate (different tubes). Each
DNA templates should have a volume of
12 μl. In case you wish that Microsynth/
Seqlab adds your sequencing primer,
please make sure that you send us a sufficient amount of your primer solution
(minimally 20 μl of a 10 μM solution; in
case you want to store your primer at
our lab, consider that each sequencing
reaction consumes at least 3 μl). DNA
samples and primers for sequencing reactions are best dissolved in pure water.
Alternatively, 10 mM Tris-HCl (pH 8) or
10 mM Tris-HCl (pH 8) with a maximum
of 0.01 mM EDTA can be used for a better long term DNA stability. Standard
TE-buffer is not suitable, because higher
EDTA concentrations inhibit polymerase
activity. Templates are stored for 1 week
whereas primers will be kept at the corresponding sequencing lab for 1year.
Sample Amounts and Concentrations
DNA Template
Concentration
Effective Amount
(in 12 µl)
1
Plasmid
60–100 ng/µl 720–1200 ng
PCR 18 ng per 100 bases in a volume of 12 µl
PCR (200bp)
3.0 ng/µl
36 ng
PCR (300bp)
4.5 ng/µl
54 ng
PCR (400bp)
6.0 ng/µl
72 ng
PCR (>400bp) etc.
etc.
Primer (pre-mixed)
2 pmol/µl 30 pmol
Primer (separate)2
10 pmol/µl = 10 µM
–
Pipetting Scheme for
Pre-mixed Option
12 µl DNA template
solution + 3 µl
sequencing primer
solution
1) In order to yield good sequencing results, please adjust your DNA plasmid solution within the requested concentration range. Please consider that the optimal
DNA concentration is 80 ng/µl.
2) Direct primer synthesis for sequencing possible.
Free pick-up service: Microsynth and
Seqlab have built up a growing number
of collection boxes for sequencing samples, predominantly in Austria, Germany
and Switzerland. In order to figure out
whether you can profit from our free
pick-up service, please call us or login to
our webshop and see under “View Collection Points”.
Overnight Sequencing: Customers in
Austria, Germany and Switzerland with
direct access to a Microsynth or Seqlab
collection box may benefit from our
overnight sequencing service. Samples
23
F
are processed overnight and results are
ready for download from 9 AM on in the
morning of the next working day (you
J Barcode High-Throughput
Service
Do you have relatively high numbers
of PCR products or plasmids that can
or need to be sequenced in parallel?
Then we recommend our Barcode HighThroughput Sequencing Service.
F
• Whole-plate sequencing on plasmids
or PCR products
• Read length per run: up to 1100 bases
• Price includes PCR purifications or plasmid preparations (from E. coli)
• Standard primers and up to 12 specific
primers will be added per plate free of
charge
• Convenient service: easy ordering and
overnight in-house production of specific sequencing primers
• User-friendly sample shipment: Customers with a Seqlab-Microsynth collection box in their vicinity may benefit
from cost-free shipment
• Rapid turnaround time: sequencing
time in the lab down to 3 days, depending on the amount of samples
• Direct access to support by experienced academic staff (no waiting on a
• Pre-paid barcoded 96-well plates have
no expiration date and can be used by
multiple researchers
will be informed by e-mail once your results are available). Please contact us in
order to experience, if an overnight service is possible for your location.
• Each of our yellow barcode labels allows unambiguous sample plate identification
then perform a longer incubation on our
side.
Sample Requirements
Non-purified PCR Products
PCR reactions can be sent directly after PCR in their reaction buffer liquid at
room temperature (RT) in the barcoded
96-well plate. The only requirement is
that you check the quality of the sample
with an agarose gel (a random subset is
sufficient; at least one sample per PCR
primer pair) before shipment. Please
send us the gel image together with the
plate or in a separate e-mail. In order
to obtain optimal sequencing results it
is important that all samples are in the
same range of concentration with respect to their lengths.
E. coli Cells (for Isolation of Plasmids at
our Laboratories)
If you send us E.coli cells, we recommend
you that you ship them in the barcoded
96-well plate within Luria Broth (LB) medium at RT. Please make sure that your
cells are incubated in 150 µl LB medium
(containing the appropriate antibiotics!)
for 3–4 hours with gentle shaking at 37°
C prior to shipping. If no shaker is available at your lab, please let us know. We
Glycerol Stocks (Additional Service for
a Fee)
Please indicate in advance if you want
us to make glycerol stocks for you. Shipment of glycerol stocks to customer
will be on dry ice. Alternatively, glycerol
stocks can be easily produced in your lab
after an overnight incubation.
Shipment
Safe shipment of liquid cultures or solutions requires good sealing of your 96well plate. It is recommended that you
seal your barcoded 96-well plate with
8-cap stripes, 96-cap mats or heat sealing.
General Information
When forwarding us purified plasmids or
PCR products, please send them in liquid
form at RT in pure water, 10 mM Tris-HCl
(pH: 8.0) or 10 mM Tris-HCl (pH: 8.0 with
a maximum of 0.01 mM EDTA). Standard
TE buffer is not suitable for sequencing.
We strongly recommend that you measure from a random subset of samples the
concentration. Again, it is very important
that all templates are in the same range
of concentration.
DNA Template
Template Volume
Plasmid
PCR
Primer (pre-mixed)1
Primer (separate)
Amount/Concentration
At least 10 µl
80 ng/µl
purified & unpurified PCR product: 1.5 ng/µl (per 100 bases)
20 pmol in 10 µl
10 µM primer aliquots2
1) Unless you use one or several of our standard primers or specific primer(s) stored at Microsynth or Seqlab.
2) Minimum volume is 200 µl.
24
 High-Throughput Service — Large-Volume Orders
Do you have large numbers (≥240) PCR
products or plasmids that can or need to
be sequenced in parallel? And you have
further come to the conclusion that our
Barcode High-Throughput Sequencing
Service is not an option for you? Then
we recommend our large-volume sequencing service in 96-well plates (includes also ready-to-load sequencing
samples). Depending on the number of
sequencing reactions to be ordered, you
will benefit from volume-dependent discounts (you need to have minimally 240
sequencing samples which equals 5 96well plates with each plate containing
minimally 48 samples).
•Whole-plate sequencing on plasmids
or PCR products
•Standard primers and up to 12 specific
charge.
•Convenient service: easy ordering and
overnight in-house production of specific sequencing primers.
•
User-friendly sample shipment: customers with a Microsynth/Seqlab collection box in their vicinity may benefit
from cost-free shipment.
•
time in the lab down to 3 days, depending on the amount of samples.
•
•Additional services upon request (additional charge will be necessary):
–Clone picking into 96-well plates and
generation of glycerol stocks
–PCR purifications or plasmid preparations (from E. coli) on request
–
Manual editing of your chromatograms by an experienced staff scientist
–Project-based mutation reports
•Special offer required: please first
contact us at Microsynth or Seqlab and
request an offer!
Sample Requirements
Purified PCR Products and Plasmids
concentration. In order to obtain optimal
sequencing results it is important that all
templates are in the same range of concentration.
Non-purified PCR Products (Additional Service for a Fee)
PCR reactions can be sent directly after PCR in their reaction buffer liquid at
room temperature (RT) in a 96-well plate.
PCR purification will then be performed
at Microsynth/Seqlab. Only requirement
is that you check the quality of the sample with an agarose gel (a random subset is sufficient; at least one sample per
PCR primer pair) before shipment. Please
send us the gel image together with the
plate or in a separate e-mail. It is important that all samples are in the same
range of concentration in respect to their
lengths.
Isolation of Plasmids (Additional Service for a Fee)
If you send us E. coli cells, we recommend you that you ship them as single
colonies on agar plates or in a 96-well
plate within Luria Broth (LB) medium at
RT. Please make sure that your cells are
incubated in 150 µl LB medium (containing the appropriate antibiotics!) for
3–4 hours with gentle shaking at 37° C
prior to shipping. If no shaker is available at your lab, please let us know. We
then perform a longer incubation on our
side. If your isolated plasmid DNA should
be sent back to you, please let us know
early enough (prior to processing).
Clone Picking and Glycerol Stocks (Additional Service for a Fee)
Please let us know if you want us to pick
clones from agar plates (max. 150 clones/
plate) and fill them into 96-well plates.
Let us also know in advance if you want
us to generate in addition glycerol stocks
for you. Shipment of glycerol stocks to
customer will be on dry ice.
96-well Plates to be used and its Shipment
It is important that you use conical 96well plates. Safe shipment of liquid cultures or solutions requires good sealing.
It is recommended that you seal your 96well plate with 8-cap stripes, 96-cap mats
or heat sealing.
General Information
concentration. Again, it is important that
all templates are in the same range of
concentration.
25
F
DNA Template
Template Volume
Plasmid
PCR
Primer (pre-mixed)1
Primer (separate)
Amount/Concentration
At least 10 µl
80 ng/µl
purified & unpurified PCR product: 1.5 ng/µl (per 100 bases)
20 pmol in 10 µl
10 µM primer aliquots2
1) Unless you use one or several of our standard primers or specific primer(s) stored at Seqlab-Microsynth.
2) Minimum volume is 200 µl.
F.2.2
Standard Segment
Are you looking for an experienced
Sanger DNA sequencing service that is
capable of sequencing routine samples
such plasmids or PCR products? And are
you further expecting the highest possible degree of flexibility, e.g. you don’t
want to invest in pre-paid barcode labels or barcoded plates. Then our Standard Segment is right for you.
F
J Economy Run Service
Your sequencing demand for routine sequencing samples such as PCR products
or plasmids is straightforward? And you
have further come to the conclusion that
our Barcode Economy Run Service is not
an option for you? Then we advise taking
a closer look at our Economy Run Service where you don’t have to purchase a
certain number of barcode labels in advance.
• Standard primers and specific primers
will be added free of charge
• Failed reactions will be repeated on request free of charge
26
expect a high level of quality since all
your sequencing reactions are monitored very closely for signal strength,
length of read and quality values.
e-mail and phone: do you have questions regarding your proposed applica-
• User-friendly and cost-free sample
shipment: Just use either the Microsynth/Seqlab pick-up service or request our pre-paid and pre-addressed
envelopes for cost-free shipment via
post mail (not available for all countries, just ask us for availability).
time in the laboratory <24h
• Direct access to support by experienced academic staff (no waiting on a
• High degree of flexibility: no need to
acquire pre-paid barcode labels in advance. You will be charged after using
this service.
• Easy labeling: either you stick your own
hand-written label or our blue nonprepaid barcode labels on your sample
tube (can be requested at Microsynth/
tion/experiment or the experimental
outcome? Then e-mail or phone us and
we will do our best to support you.
• No minimum order size
Seqlab for clear and convenient labeling)
Sample Requirements
Same as for our Barcode Economy Run
Service (see page 23)
pick-up service, please call us or login to
our webshop and see under “View Collection Points”.
 High-Throughput Service
Do you have relatively high numbers
(≥48) of PCR products or plasmids that
can or need to be sequenced in parallel?
And you have further come to the conclusion that our Barcode High-Throughput Sequencing Service is not an option
for you? Then we recommend our HighThroughput Sequencing Service for 96and 384-well plates.
•Whole-plate sequencing on plasmids
or PCR products
 Ready-to-Load Sequencing
If you have a workflow in your lab for
sample preparation, cycling and purification and just want to outsource the actual analysis, this service is right for you.
•
User-friendly sample shipment: Customers with a Microsynth or Seqlab
collection box in their vicinity may benefit from cost-free shipment.
•Standard primers and up to 12 specific
charge
•Convenient service: easy ordering and
overnight in-house production of specific sequencing primers.
•
User-friendly sample shipment: Customers with a Microsynth/Seqlab collection box in their vicinity may benefit
from cost-free shipment
•
time in the lab down to 3 days, depending on the amount of samples
•
•Additional services upon request (additional charge will be necessary):
–Clone picking into 96-well plates and
generation of glycerol stocks
–PCR purifications or plasmid preparations (from E. coli) on request
–
Manual editing of your chromatograms by an experienced staff scientist
–Project-based mutation reports
•
time in the lab down to 28 h, depending on the amount of samples
•
•Dried samples in Micro Amp Optical
96-well or 384-well reaction plates with
barcode from Applied Biosystems (or
compatible plates)
Sample Requirements:
•Sample preparation, cycling and purification according to protocols from Applied Biosystems
Sample Requirements
See the section “High-Throughput Service — Large-Volume Orders” on page
25.
96-well or 386-well plates can be provided upon request.
F.2.3 Premium Segment
Are you looking for a Sanger DNA
sequencing service that provides more
than standard features? Then our Premium Segment is right for you.
•Premium quality: the DNA concen
tration of all DNA templates is measured, and customized amounts are
used for each individual sequencing
reaction. This results in a major improvement of sequencing quality.
Adapted protocols for different template types are used for further quality
improvement.
•Total quality control: every sample
is checked individually for in-depth
monitoring of the sequencing quality.
Individual tests are undertaken in order to elucidate the measures needed
to improve the sequencing quality
(additional purifications, fresh sample
preparation, new primer synthesis, etc.)
•Extended Certificate of Analysis
available and/or customized documentation
•Technical support & consulting via
e-mail and phone: we will be happy
to advise you on your experiments and
work with you towards achieving suc-
cessful sequencing results. Just send
us an e-mail or phone us, and we will
use our most sophisticated methods.
•R&D available for specific projects:
issue-solving involving all divisions
(i.e. DNA Sequencing, DNA Synthesis,
DNA Extraction, PCR Amplifications,
Real-Time PCR, Genotyping, etc.)
•Additional
services
available:
whether picking your clones from an
agar plate or purifying your PCR products, we offer flexible additional services to meet your needs.
27
F
J Premium Run Service
Are you looking for a personalized sequencing service that includes comprehensive customer support and
troubleshooting? Are you looking for a
top-quality sequencing service that is
able to decode even difficult sequences?
Then we recommend taking a closer look
at our Premium Run Service.
• Standard primers and specific primers
will be added free of charge.
time in the lab down to 28 h
• Failed reactions will be repeated free of
charge.
• Comprehensive support and troubleshooting via our experienced academic
staff (no waiting on a recorded-message hotline):
– Depending on your requirements,
sequences can be delivered as edited or non-edited. Editing includes
–
–
–
–
a manual proofread of your chromatogram by our experienced staff.
Software-derived mistakes or uncertainties resulting from base calling (this is the procedure where the
chromatogram is translated into
your sequence) will be corrected.
Upon receiving your samples, we
will check the DNA concentration; if
DNA concentration is too low, we will
approach you to discuss the further
proceeding.
Depending on your requirements,
results are provided via e-mail or
via download from a HTTPS server.
FASTA files are attached to the chromatograms.
Paper printouts are made available
upon request.
In case of failed or poor sequencing results, we will approach you
and make useful suggestions for issue solving (e.g. poly stretches, high
G/C content, hairpin structures etc.).
However, whether we continue with
sequencing or stop at this stage is always your decision.
– User-friendly and cost-free sample shipment: Just use either Microsynth’s or Seqlab’s pick-up service
or request our pre-paid and preaddressed envelopes for cost-free
shipment via post mail.
• Additional services:
– One-Drop Sequencing
– Special Treatment
– Plasmid Preparation from E. coli
– PCR Purification
Sample Requirements
General Information
Each DNA sample and each primer must
have a minimum volume of 20 µl. DNA
samples and primers for sequencing reactions are best dissolved in pure water.
Alternatively, 10 mM Tris-HCl (pH 8) or
10 mM Tris-HCl (pH 8) with a maximum
of 0.01 mM EDTA can be used for a better long term DNA stability. Standard
TE-buffer is not suitable, because higher
EDTA concentrations inhibit sequencing
polymerase activity. DNA samples will be
stored for 3 months, whereas primers will
be kept at Microsynth for 1 year.
F
DNA Template
Plasmid
PCR (> 5000bp)
PCR (< 5000bp)
PCR (< 1000bp)
PCR (< 500bp)
PCR (< 200bp)
Primer
28
Concentration
100 ng/µl
100 ng/µl
40 ng/µl
20 ng/µl
10 ng/µl
5 ng/µl
10 pmol/µl = 10 µM
Effective Amount
(in 20 µl)
2 µg
2 µg
0.8 µg
0.4 µg
0.2 µg
0.1 µg
200 pmol
pick-up service, please call us or login
to our webshop and see under “View
Collection Points”. For most customers
without a Microsynth or Seqlab collec-
For each additional
reaction
+ 5 µl
+ 5 µl
+ 5 µl
+ 5 µl
+ 5 µl
+ 5 µl
+ 5 µl
tion box close by, we can offer convenient and cost-free shipment of samples
via our pre-apid and pre-addressed envelopes.
 Primer Walking Service
Do you need the complete sequence of
a plasmid insert or any other DNA template which is longer than 1500 bp? Then
we recommend using one of the following primer walking services:
•Non-assembled Primer Walking Service (single-stranded and doublestranded)
Upon sequencing your template, you
will receive the single sequences. Final
assembly will have to be done at your
end.
•Assembled Primer Walking Service
(single-stranded and double-stranded)
Upon sequencing your template, assembly of the single sequences will
be completed quickly and accurately
at Microsynth/Seqlab. You will receive
an electronic and printed version of the
aligned sequence.
•Primer Walking Service for Sequence
Verification (single-stranded and
double-stranded)
Upon sequencing your template, we
will do first assembly of the single sequences and then verify the obtained
sequence against your original sequence. You will receive an electronic
and printed version of the aligned sequence as well as a description of discrepancies.
actions. Since we are able to produce the
sequencing primers in-house, we achieve
a relatively high sequencing speed. On
average, we perform one sequencing
reaction per day. If you choose the double-stranded service, both strands are
sequenced to confirm every established
base. Our double-stranded sequencing
service produces a sequence accuracy of
99.999% for standard templates, i.e. less
than one error in 100’000 base pairs of
sequence (publication quality).
In general, your DNA template is sequenced by a series of primer walking re-
Main Service Features and Benefits for all Primer Walking Services
Non-Sequence
assembled AssembledVerification
ParameterSS1DS2SSDSSSDS
Fast in-house design and synthesis of primers
x
x
x
x
x
x
Delivery of synthesized sequencing primers on request
x
x
x
x
x
x
Read length per run: up to 1100 bases
x
x
x
x
x
x
Fast sequencing with 1 run per day on average3
xxxxxx
Editing of sequences
xxxxxx
Delivery of electronic files such as project data sheet
x
x
x
x
including sequencing strategy, text files and
chromatograms for each single reaction
Delivery of chromatograms for each single reaction
x
x
x
x
x
x
Accurate assembly of single sequences
x
x
x
x
Verification of an assembled sequence against
x
x
its original sequence
1) SS stands for single-stranded.
2) DS stands for double-stranded.
3) For instance, a 3 kb DNA sequence can be decoded within 5 days.
 Large Construct Sequencing
Do you need an experienced Sanger sequencing service for larger constructs
such as BACs, PACs, FOSMIDs, COSMIDs
and genomic DNA? Then we suggest taking a closer look at our Large Construct
Sequencing Service.
•Standard primers and specific primers
will be added free of charge.
•
time in the lab down to 52 h per reaction
•Failed reactions will be repeated free of
charge.
•Additional service: BAC, PAC, FOSMID
and COSMID DNA isolation from E. coli
(extra charge will be necessary)
•Various sequencing options feasible:
29
F
– Partial Sequencing of BACs, PACs,
FOSMIDs and COSMIDs: you can
choose between single sequencing
runs and primer walking reactions.
Moreover, you can either send us
your isolated DNA of interest or your
E. coli clones.
– Partial Sequencing of Genomic
DNA: you can choose between single sequencing runs and primer
J Clone & Sequence
PCR amplification of heterogeneous biological samples results in a heterogeneous mixture of PCR products (e.g. ribosomal 16S PCR generated from stool or soil
samples). In order to be able to sequence
individual PCR products by DNA Sanger
sequencing, it is first necessary to clone
them. At Microsynth, we are able to per-
J Exon Sequencing & Mutation Detection
Are you interested in identifying (point)
mutations in genes or exons with great
accuracy on a nucleotide level? Then we
recommend our Exon Sequencing & Mutation Detection Service.
F
J GLP-Compliant Sequencing
Microsynth/Seqlab can offer high quality double strand sequencing compliant
with Good Laboratory Practice (GLP),
as specified for non-clinical laboratory
studies. Typical applications are submissions to the FDA or patent submissions.
All our processes are performed according to proprietary standard operating
procedures. To ensure the quality of our
GLP-compliant sequencing service, we
are routinely assessed by process audits.
• You have the choice between 2-fold or
4-fold coverage
30
walking reactions. To obtain good sequencing results, it is important that
you provide us with genomic DNA of
high quality which is not larger than
4–5 MB.
– Entire Sequencing of BACs, PACs,
FOSMIDs and COSMIDs: large constructs can be sequenced to x-fold
defined coverage or publication
quality either by using conventional
Sanger sequencing or by next generation sequencing approaches.
Please contact us and we will discuss
with you how to best address your
sequencing project.
– Entire Sequencing of Whole Genomes: please see the NGS section
on page 31.
form the entire process of cloning and
sequencing, no matter how many clones
your sequencing project may require.
approach allows to circumvent the cloning step and becomes more economical
with increasing sample numbers and
throughput requirements. Please contact us to figure out which approach fits
best your needs.
Beyond Sanger DNA sequencing, we are
also able to offer you comprehensive
next-generation sequencing services. In
general, a next-generation sequencing
• Project management and consulting
• PCR amplification of exons
• Double-stranded sequencing of the resulting PCR products
• Mutation reports
• Each project is guided by a designated
study director who oversees all the
steps
• Quality control of incoming DNA
• Design of sequencing primers every
700 bases (2-fold coverage) or 300–400
bases (4-fold coverage), in-house synthesis of these primers
• Complete double stranded sequencing
of the region of interest with at least 2
or 4 fold coverage
• Evaluation of each chromatogram.
Only sequences with quality values
>30 (base call accuracy higher than
99.9%) are used for the assembly
• Assembly of sequence data
• Sequence verification against a known
reference sequence or de novo sequencing
• Guaranteed accuracy of final data:
2-fold coverage (>99.999%), 4-fold coverage (>99.99999%)
• Extended sequencing project documentation
• Detailed sequencing strategy
• Quality assurance statement (ISO/IEC
17025 (STS 429))
• Documents signed by the study director
• Archiving of samples and data for 10
years (longer times available on request)
 Additional Services
Beyond the various DNA sequencing
services, Microsynth/Seqlab offer a variety of useful additional services to make
your life easier that are suitable for decoding even difficult-to-sequence regions/samples. In general you can select
between the following four services (are
only available in combination with our
Premium Run Service or High-Throughput Service):
1. Special Treatment
Our Special Treatment Service is especially useful if you want to decode
difficult-to-sequence constructs such as
regions containing hairpin structures,
G/C-rich sequences, etc.
Continuous optimization of our Sanger
sequencing capabilities over the last
22 years has resulted in protocols that
are able to map difficult or even very difficult DNA templates with a success rate
>98%.
Generally, we recommend the following
two-stage approach to our customers:
•Special Treatment Service – Stage 1:
for difficult-to-sequence samples
•Special Treatment Service – Stage 2:
for very difficult-to-sequence samples
2. One-Drop Sequencing
Our One-Drop Sequencing Service is especially helpful if you want to sequence
plasmid DNA but don’t have sufficient
DNA. By applying this type of service, we
are able to perform sequencing if you
provide us with 50 ng or at least 1 µl of
your DNA (one drop). It takes only one
additional day. Therefore, the usual duration for entire sequencing of plasmid
DNA will be 2 days.
3. DNA Preparation from E. coli
Single Plasmid Preparation Service
You send us your E. coli cultures as single
colonies grown on agar plates stating the
antibiotic resistance. We pick your clones
and amplify them before we isolate the
plasmid DNA to be sequenced.
Please Note:
E. coli cultures arriving at Microsynth/
Seqlab before 12:00 AM will be picked
the same day. Plasmid preparation takes
only one day. Therefore, the first sequencing results can be expected usually after 2 working days.
High-Throughput Plasmid Preparation Service
Plasmid preparations will be performed
in 96- or 384-well plates. For E. coli cells,
we recommend sending them in 96- or
384-well plates as frozen glycerol stocks
or in Luria Broth (LB) medium at room
temperature (good sealing necessary!).
BAC, PAC, Fosmid, Cosmid DNA Preparation Service
You send us your E. coli cultures as single
colonies grown on agar plates or as stab
cultures stating the antibiotic resistance.
We pick your clones and amplify them
before we isolate the DNA templates to
be sequenced.
4. DNA Purification
Purification Service for Plasmids
Plasmid DNA is purified by ethanol precipitation.
Purification Service for PCR Products
PCR primers and leftover dNTPs are removed from your PCR reactions. Please
be aware that this purification service
does not separate individual PCR fragments (no gel extraction)!
F
31
F.3
F.3.1
Overview
Microsynth offers a wide range of comprehensive next-generation sequencing
(NGS) services based on several state-ofthe-art NGS platforms:
• Illumina
• PacBio
• SOLiDWildfire
• 454/Roche
Next-generation sequencing at Microsynth means that you will get much
more than the access to state-of-theart NGS technologies. It is the profound
expertise of more than 20 years in DNA
sequencing as well as related molecular
biology knowledge such as DNA/RNA
isolation, PCR/realtime PCR analysis and/
or synthesis of DNA oligos, which you
can rely on.
In addition, you can expect extensive
consultation during the entire phase of
your NGS project. A study manager is
interacting with you but also internally
with a team of molecular biology experts
to ensure that your project is optimally
designed and carefully executed.
Genome
Sequencing
Transcriptome
Sequencing
• Reference Transcriptome
Generation
• Differential Gene
Expression Analysis
• Small RNA Sequencing
F
•
•
•
•
•
De Novo Sequencing
Resequencing
Targeted Resequencing
ChIP Sequencing
Epigenome Sequencing
Bioinformatics
and more…
Metagenome
Sequencing
• State-of-the-art bioinformatics
• Extensive project consultation
• Full molecular biology service
(e.g. DNA/RNA isolation, qPCR,
primer design & synthesis)
• Bacterial Community Analysis
• Fungal Community Analysis
• Complete Metagenomes
Amplicon
Sequencing
• 16S/18S rDNA Sequencing
• ITS Sequencing
• Customized Deep Sequencing
32
Once your data will have been generated, you can make use of our in-depth
bioinformatics knowhow and solutions.
Hence, your sequencing project will be
in good hands at Microsynth and we do
everything possible to deliver you highquality results where you can build on
your further ongoing scientific work.
F.3.2Applications
Microsynth can offer you a broad spectrum of applications in the area of next
generation sequencing (see table below). Moreover, due to the availability of
most of the well-known NGS platforms,
Microsynth is also able to consult you
in picking the right technology for your
a pplication.
The table gives you a rough guideline
how we see the potential of an individual
NGS platform. However, many sequenc-
ing projects may profit from a hybrid
approach using more than one NGS platform and therefore, discussing your project with our NGS experts will help you to
find the optimal approach.
Illumina
Illumina
PacBio
454
SOLiD
Applications
MiSeqHiSeq
Genome Sequencing
De novo
++ + +++++++
Resequencing
+++++++ + +++
Targeted resequencing
Whole exome
++
+++
+
+++
Customized
+++++
+ +++
ChIP Sequencing ++++ ++++
Transcriptome sequencing
Whole transcriptome
++++++
reference generation
Whole transcriptome
++++ ++++
small RNA sequencing
+
+++
+
+++
Metagenomic Sequencing
Whole genome shotgun
++++++
++++
16s rDNA sequencing
+++
+
+
+++
ITS sequencing +++
+++++
Ultra Deep Amplicon
Sequencing
Ultra-deep sequencing
++++
+++
of specific PCR products
”+“ suitable approach
”+++“ recommended approach
Beyond producing high-quality sequencing data on our various NGS platforms,
Microsynth can offer you the following
additional services:
•Project consultation: Each NGS project is unique. In order to strive for an
optimal project design our NGS experts will discuss with you the best NGS
strategy for your project. Once we have
done together a careful project analysis, you will receive a project offer.
•Next generation sequencing related
molecular biology services:
–DNA/RNA isolation
–Library preparation
–PCR and qPCR services
–Sanger DNA sequencing
–Synthesis of DNA oligonucleotides
•Bioinformatics: Several state-of-theart analysis pipelines are available at
Microsynth (e.g. de Novo assembly,
mapping, SNP and InDel calling, differential gene expression analysis,
metagenomics analysis of bacterial or
fungal communities). In addition, more
customized bioinformatics projects
can be performed depending on the
scientific question of the researchers.
33
F
F.3.3
Practical Information
Shipping Address
Microsynth AG
Schützenstrasse 15
9436 Balgach
Switzerland
Shipment Recommendations
We recommend shipping the samples
frozen on dry ice.
Buffer Recommendations
DNA: 10 mM Tris-HCl buffer (pH 7.5–8.5)
RNA: 10 mM Tris-HCl buffer (pH 7.0)
Sample Amounts Required for Illumina Sequencing
Type of Library
DNA for Nextera XT library*
DNA for Nextera library
DNA for TruSeq library
DNA for Mate Pair library
DNA for amplicon preparation (e.g. 16s rDNA or ITS analysis)
Ready-to-sequence amplicon library
Total RNA for whole transcriptome library
Amount (µg)
>0.2
>0.5
>5
>5
>0.2
>0.2
>10
Concentration (ng/µl)
>10
>10
>50
>50
>10
>10
>200
Amount (µg)
>2
>15
>25
>0.2
>0.2
>10
>0.2
>50
>100
>200
>10
>10
>200
>10
* low input protocol as low as 1 ng is available (excludes quality control)
Sample Amounts Required for 454 Sequencing
Type of Library
DNA for shotgun library
DNA for 3kb paired-end library
DNA for 8kb paired-end library
Ready-to-sequence amplicon library *
DNA for amplicon preparation (e.g. 16s rDNA or ITS analysis)
Total RNA
Poly(A)RNA
F
* The final pool should have a total amount of amplicons of > 0.2 μg and a concentration > 10 ng/μl (and not each library in the final pool)
Sample Amounts Required for PacBio Sequencing
Type of Library
DNA Library
34
Amount (µg)
>10
>300
Sample Amounts for SOLiD Sequencing
Type of Library
DNA for fragment/paired-end library
DNA for mate-pair library
DNA for targeted enrichment (including whole exome analysis)
Total RNA for whole transcriptome analysis
Total RNA for small RNA analysis
rRNA-depleted RNA or poly(A) RNA for whole transcriptome analysis
DNA/RNA Quantification
DNA/RNA quantification is recommended to be done by a fluorometric method,
e.g. PicoGreen®, RiboGreen®, Qubit® etc.
F.3.4
Amount (µg)
>5
>20
>5
>10
>5
>0.2
DNA Quality Control
Microsynth performs on each received
sample a complete quality control prior
to further sequencing steps. However,
we do recommend that you also check
>100
>100
>100
>100
>100
>10
your DNA on a gel or on the Bioanalyzer
to allow a straightforward approach for
your sequencing project. If you do so,
please provide us with the gel picture or
trace file as well.
The Microsynth Advantage
State-of-the-art
NGS Platforms
In-depth Bioinformatics Know-how
Extensive
Project Consultation
The best thing that
can happen to a DNA
Excellent PricePerformance Ratio
F
Other Molecular
Biology Services
35
F.4
Real-Time PCR
Microsynth, a leader in the field of molecular biology, offers a broad spectrum
of real-time PCR services and products.
More than ten years of experience with
F.4.1
• Pathogenicity?
• Primer-probe set designed and validated?
• Assay established? Single or multiplex
assay?
• Expected number of samples?
• Number of replicas per sample?
• Delivery form of data (raw data, Ct values or additional interpretation)
• Accreditation required?
The individual requirements of each customer project complicate pricing. Please
inquire for your individual quote. The following questions are relevant for appropriate pricing:
• Kind of template (gDNA, cDNA, RNA)?
• DNA/RNA isolation necessary? From
what kind of organism and tissue?
• Delivery of samples (amount, quality
and vessel)?
• Gene expression analysis in any organism
• Realtive gene quantification at genomic level
• SNP (single nucleotide analysis) genotyping and analysis of polymorphisms
• Epigenetics: e.g. methylation analysis
by real-time PCR-based high-resolution
melting
• Quality and safety testing e.g. genetically modified organisms, species identification, allergen detection
• Clinical applications e.g. diagnosis of
bovine virus disease in ear tissue samples
We’ve successfully performed many different projects (small to large projects)
over the last decade, ranging from
1-month projects to projects lasting several years. Please have a look onto our
website for more information.
hesitate to contact Dr. Vital Wohlgensinger
Customized and Ready-to-Use qPCR Assays
Are you interested in a functional, specific and tailor-made real-time PCR assay?
Then we encourage you send us your target sequence or accession number. Simply leave it up to us to design, to synthesize as well as to perform functionality
testing of your primer-probe set. You will
receive your real-time PCR assay within
2-3 weeks after the order.
• Real-time PCR assays with proven functionality due to comprehensive testing
using a specific positive control as well
as a no template control
36
nucleotides qualify Microsynth as your
partner of choice for a plurality of realtime PCR services/projects.
Project-based Analysis Services
Do you want to outsource your realtime PCR measurements? We can offer
you rapid and reliable semi-quantitative
and quantitative real-time PCR measuring services based on hydrolysis probes,
SYBR-green or FRET assays. The full service includes nucleic acid isolation, assay
design and validation, target detection
and data analysis including normalization with internal controls.
F.4.2
F
customer projects of any scale, our profound understanding of DNA/RNA isolation and lab automation as well as our
in-house production facility for oligo-
• High degree of customization: you as
our customer will decide
– whether the assay should be singleplex or multiplex
– which pair(s) of possible reporter
dyes and quenchers should be selected
– which sequence areas should be
considered or not considered when
designing the primer/probe set(s)
• High sensitivity due to optimization
of PCR working conditions: we design,
synthesize and test your primer set(s)
for their PCR performance
• Easy publishing due to compliance
with MIQE1 guidelines (full transparency with respect to sequence information of used primer and probes)
• Low-cost for follow-up orders of primer/probe sets (you will be provided
with complete sequence of all oligonucleotides)
• High quantity delivered: QC-tested
primer/probe set(s) in single tubes
(aliquoted) are sufficient for more than
2000 PCR reactions
•Gene expression analysis in any organism
•Gene quantification at genomic level
•SNP (single nucleotide analysis) genotyping and analysis of polymorphisms
hesitate to contact Dr. Vital Wohlgen
singer
1 Bustin, S. A.; Benes, V.; Garson, J. A.; Hellemans,
J.; Huggett, J.; Kubista, M.; Mueller, R.; Nolan, T.;
Pfaffl, M. W.; Shipley, G. L.; Vandesompele, J. &
Wittwer, C. T. The MIQE Guidelines: Minimum
Information for Publication of Quantitative
Real-Time PCR Experiments Clinical Chemistry,
2009, 55, 611–622
F.4.3 Multiplex qPCR Assays for Advanced Food Testing
Do you want to trace or quantify marker
genes of animal specific, allergenic or
transgenic background in food samples?
•Growing number of allergen-, species-,
GMO- and microorganism-specific kits
•
Validated qPCR assays1 (multiplex,
quantitative, highly specific)
•
Ready-to-use kits with detailed SOP:
just solubilize the primer/probe mix-
ture in dd H2O and add your PCR Mastermix (not included)
•
High efficiency (assay with up to 5
markers in one PCR run!)
•High quantity delivered: 1 kit contains
5 tubes with primer/probe sets for 5 x
20 PCR reactions (25 µl volume)
• Excellent price/performance ratio
or obtaining a quote? Then please visit
our website and/or get in contact with
Dr. Vital Wohlgensinger
• Food quality and safety testing
• Allergen detection
1 All kits have been developed in collaboration
with Dr. René Köppel from the Zurich Cantonal Laboratory – an acknowledged expert on
the use of cutting-edge analytical systems
for food safety testing. Under his supervision,
each assay has been fully validated, and even
tested in interlaboratory trials.
Multiplex qPCR Kits for Animal Classification and Meat Testing
Product Name
AllMeat
AllHorse
AllMilk
AllPaté
AssignAnimal
Assay Type
Marker 1
Marker 2
Marker 3
Marker 4
Tetraplex
Chicken
Pork
Beef
Turkey
Tetraplex
Sheep
Pork
Beef
Horse
Tetraplex
Cow
Goat
Sheep
Water buffalo
Pentaplex
Chicken
Duck
Goose
Turkey
Classification of animal species in combination with Sanger sequencing (cytochrome b)
Marker 5
n.a.
n.a.
n.a.
Pork
Multiplex qPCR Kits for Allergen Testing
Product Name
AllAll A
AllAll B
AllAll G
Assay Type
Tetraplex
Tetraplex
Tetraplex
Marker 1
Peanut
Cow‘s milk
Lupine
Marker 2
Celery
Almond
Almond
Marker 3
Soybean
Chicken egg
Para Nut
Marker 4
Hazelnut
Sesame
Sesame
Marker 5
n.a.
n.a.
n.a.
Marker 2
35S Promotor
Bar gene
Mon89788
DP356043-5
Mon863
Nk603
Marker 3
Soy (lectin)
CP2/CP4/EPSPS
Soy (Le1)
Lectin
T25
Ly038
Marker 4
Maize (mhmg)
Pat Gene
Soy2704
CV127-9
Maize (mhmg)
Maize (mhmg)
Marker 5
CaMV
n.a.
A5547-127
Mon87701
Mon810
Bt176
Multiplex qPCR Kits for GMO Testing
Product Name
AllGVOScB
AllGVOScC
AllSoyA
AllSoyB
AllMaize C
AllMaize D
Assay Type
Pentaplex
Tetraplex
Pentaplex
Pentaplex
Pentaplex
Pentaplex
Marker 1
Nos Terminator
FMV Promotor
RoundupReady
DP305423-1
Starlink CBH
Bt11
37
F
Multiplex qPCR Kits for Bacteria Testing
Product Name
AllBakA IPC*
Assay Type
Pentaplex
Marker 1
E. coli Stx1 Stx2
intimin
Marker 2
Salmonella
(incl. bongori)
AllCamp
Tetraplex
AllColi
Tetraplex
Campylobacter
jejuni
E. coli spp
Campylobacter
lari
E. coli
eae/intimin
Marker 3
Listeria
monocytogenes
Campylobacter
coli
E. coli Stx1
Marker 4
Campylobacter
spp
Marker 5
IPC pUC19
IPC pUC19
n.a.
E. coli Stx2
n.a.
* white and black mustard
F.5
Genotyping
Since 2003 Microsynth has been offering
various routine as well as project-based
genotyping services, especially those
based on fragment length analysis of
F.5.1
Service Description for Fragment
Length Analysis:
• Design and synthesis of high quality
fluorescent-labeled PCR primers for individual or multiplex strategies via our
in-house oligonucleotide production
facility
• Optimization of PCR amplification conditions (e.g. for detecting STRs)
• PCR amplification of STR loci and separation on state-of-the art capillary electrophoresis systems (e.g. ABI 3730xl)
• Allele size and identity determination
with GeneMapper ID software
• Data presented in user-friendly spreadsheets that contain fragment length/
38
production facility for oligonucleotides
qualify Microsynth as your partner of
choice for a variety of genotyping questions.
allele size and other parameters of interest
• Data or main results are made available
in electronic or hard copy formats; additional information such as electropherogram for publication matters can
be made available upon request.
• Experience with difficult-to-assay samples and complete assistance with data
interpretation
• A “ready-to-load“ service is available on
our capillary electrophoresis system if
the user has prepared the fluorescently
labeled PCR products in 96-well plates
• Expected number of samples (single
analysis, repeated analysis)?
• Delivery of samples (amount, quality
and vessel)?
• Assay established?
• Single or multiplex assay?
• Number of replicas per sample?
• Delivery form of data (raw data, analysed data, report)
• Test samples available? Especially in
case of larger projects, we prefer to
perform initial testing in order to make
a good bid.
Fragment Length Analysis
Do you want to outsource your fragment
length analysis? Whether your application is a plain routine service or more
complex R&D, Microsynth can offer you
both the know-how and the necessary
lab infrastructure.
F
short tandem repeats (STR). Our solid
experience in this area, our profound understanding of DNA/RNA isolation and
lab automation as well as our in-house
The very individual requirements of each
customer project complicate pricing.
Please request an individual quote. The
following questions are relevant for appropriate pricing:
• DNA/RNA isolation necessary? From
what kind of organism and tissue?
hesitate to contact Dr. Georges Wigger
F.5.2 Human Cell Line Testing
Cross-contamination and misidentification of mammalian cell cultures is widespread, affecting an estimated 15–20%
of the cell lines currently used in biomedical research. Several high-impact
journals are already refusing to review
submitted manuscripts unless they contain information on the authentication of
cell lines used in a study, and in the near
future similar restrictions are likely to be
applied to grant applications as well.
Report which includes all American Type
Culture Collection (ATCC) standard markers for cell line authentication.
Microsynth can characterize your human
cell line by analyzing a set of STR markers
(PowerPlex®16HS). Upon testing your cell
line we will provide you with a STR Allele
hesitate to contact Dr. Georges Wigger
F
39
G
G.1
Our Know-how for Your Success
In today’s competitive environment, the
pharmaceutical, life sciences and biotech
industries as well as academic/public
institutions are increasingly forced to reduce costs and become leaner. As a consequence, the percentage of R&D work
to be outsourced is increasing. This trend
will continue to be driven by the pursuit
of improving R&D cost efficiency as well
as efficacy. In other words, doing more
R&D with less, and doing it smartly!
Microsynth has vast experience in providing a broad spectrum of outsourcing
services for life sciences clients – from
start-up biotechnology firms, large multinational pharmaceutical companies to
renowned research hospitals and scientific institutions.
Therefore we encourage you to do what
you do best and outsource the rest! We
offer our expertise in these areas:
• DNA/RNA isolation from various sources
• Design and synthesis of DNA and RNA
oligonucleotides (unmodified, modified, various purification methods)
• Design, synthesis and validation of
primer probe sets for Real-Time PCR
• Sanger DNA sequencing and next-generation sequencing Illumina, PacBio,
SOLiD Wildfire, 454/Roche
• (High-throughput) PCR or Real-Time
PCR and Genotyping
• High-throughput cloning
• Laboratory automation
• Bioinformatic and data analysis
• Project management
Project Management
Laboratory Automation
Database Management
Data Analysis
DNA/RNA Synthesis
DNA/RNA Oligos
Premium Oligos
Antisense Oligos
Dual-labeled Probes
siRNA
Various Design Services
Interested in receiving more information? Then please have a look on our
homepage. You will find some selected
G.2
G
project examples as well as customer
testimonials. Or just approach Dr. Tobias
Schmidheini either via e-mail
([email protected])
or via phone (+41-71-722 83 33).
lasting several years. In the following
you will find 3 selected project examples which shall give you a first insight
of our know-how and experience in pro-
ject outsourcing. More examples can be
found on our website.
Project Examples
Microsynth has successfully performed
many different projects (small to large
projects) over the last decade, ranging
from one-month projects to projects
40
DNA & RNA Isolation
Sanger Sequencing
PCR & qPCR Applications
Genotyping
High-Throughput Cloning
G.2.1 Eradication of Bovine Virus Diarrhoe
Project Realization
The challenges associated with the BVD
eradication program was to establish
a robust logistics covering the full process of (i) sample shipment over (ii) costefficient diagnosis of the BVD virus from
ear notches including thorough QA/QC
systems to (iii) upload of the results to
federal databases with the possibility to
screen up to 10,000 ear notches per day.
In a first step, Microsynth joined roundrobin testing of the Swiss Veterinary Office and has got accredited according to
EN ISO17025 STS 429. It is worth mentioning that Microsynth has been one of
the few labs that approached BVD testing by applaying a highly sensitive qPCR
assay. In a second step, the logistics for
high-throughput diagnosis of BVD from
ear notches including a QA/QC system
Livestock Owners
(> 5.000)
Veterinary
Authorities
EN ISO 17025 STS 429
Project Outline
BVD is one of the most widespread and
economically important cattle diseases,
causing annual losses of > 10 M in Switzerland. Therefore, the Swiss government
set-up an eradication program which included the testing of the complete cattle
livestock (first phase) and subsequently
monitored all newborn calves during
several years (second phase). Microsynth
was successful to become one of a few
laboratories which were accredited by
the Swiss government to qualify for BVD
testing. Further, Microsynth signed exclusive contracts with 5 Swiss cantons.
Unpack Ear Notches
and Arraying
Resolve Pools for
positive Samples
Fast BVD
RNA Lysis
RT-qPCR
Analysis
Pooling
Data Analysis
RT-qPCR
Data Tranfer to
Federal Databases
for monitoring the quality and sensitivity
of the diagnosis was set up. Finally, Microsynth obtained the responsibility for
exclusively screening of BVD in 5 Swiss
cantons for several years. Thereby, it became the lab that has analyzed by far the
the most ear notches during the initial
and the monitoring phase of the eradication program.
Customer Feedback
„The eradication program for BVD which
started in 2008 is bearing fruit. To trace
and eliminate the remaining infected
cattle (less than 0.2%), all newborn calves
will be screened until sufficient certainty
regarding eradication is achieved. This
is a great success that would not have
been possible without the excellent collaboration of the Swiss Veterinary Service
with the selected laboratories that have
been accredited for this type of testing.
In this aspect it is fair to mention that Microsynth was by far the largest laboratory
handling more than 800,000 samples up
to now, and in peak times up to 10,000
samples per day; always in an excellent
quality.“
Dr. Elena Di Labio,
Swiss Federal Veterinary Office FVO
G
41
G.2.2 Metagenomic Analysis of Gut Microbiota
Project Realization
In a first step Microsynth established a
robust isolation method for DNA from
stool samples including extensive quality controls in cooperation with the
customer. The isolation method was
finally adopted for a high-throughput
approach. In parallel, different variable
gene regions of the 16S rDNA were selected for PCR and comparisons were
run to decide which region serves best
the customer needs. Further R&D was
performed to define a 454 sequencing
strategy which meets the customer requirements regarding the number of
G
42
Customer
Stool Samples
High-Throughput
DNA Isolation
Selection of
Suitable Region
16S rDNA
Amplification
Quantification and
Pooling
Design & Synthesis of
454 Fusion Primers
454 Sequencing of
Amplicon Pools
MID-Filtering
Bioinformatic
Analysis
reads in a cost-efficient way. 454 fusion
primers were designed and synthesized
in house to allow pooling of hundreds
of stool samples during a single 454
run. The down-stream bioinformatics
analysis included the development of
customized analysis pipeline allowing to
analyze the community structure of the
gut microbiotas. Finally, a analysis report
including OTU and taxonomy lists, and
community comparisons were delivered
to the customer.
Down-Stream
Community Analysis
Delivery of Analyzed Data (OTU Lists, Taxonomy, Heat Plots, ...)
Project Challenge
The analysis of 16S rDNA amplicons from
microbial communities by means of 454
sequencing has become an essential
toolkit to evaluate the microbial diversities. An industrial customer wanted us to
perform comprehensive analysis of the
gut microbiota. Microsynth was faced
with four major challenges that had to
bee overcome: (i) high-throughput isolation of high-quality DNA from samples
(stool is one of the most difficult matrices
in this context!), (ii) the selection of suitable variable 16S rDNA regions for 454
sequencing, (iii) design and evaluation
of a robust PCR system, and (iv) set-up of
an analysis pipeline for proper processing and evaluation of next generation
sequence data to obtain high-quality
data delivered in form of a user-friendly
report.
Customer Benefits
• Microsynth could offer a cost-efficient
one-stop solution; all deliverables from
one source
• Regular contact with customer to make
sure project definition and accomplishment is in accordance with customerspecific requirements
• Application of state-of-the-art molecular biology technologies and bioinformatics know-how to overcome all 4
project challenges
G.2.3 Detection of Cow & Pig DNA in Heparin
Project Realization
In a first phase, a protocol for specific
digestion of heparin was initially established and validated. Then, a thorough
qPCR assay strategy was defined, which
on the one hand allows to detect porcine & bovine traces of DNA in heparin
samples and on the other hand allows
to assess the quality/completeness of
the heparin digest. A triplex qPCR assay
approach was selected which simultaneously detects a cow-specific, a pigspecific as well as an internal control
Customer
Heparin Samples
Set-up & Validation
Routine Testing
Heparin Digest
(QC by qPCR)
Heparin Digest
Design & Synthesis
of qPCR Assays
qPCR Analysis
(including QA/QC)
Validation of
qPCR Assays
Data Analysis &
Reporting
Delivery of Results as
Specified by Customer
Project Challenge
Heparin is widely used as an injectable
anticoagulant and as anticoagulant coating on various experimental and medical
devices. Pharmaceutical grade heparin is
derived from mucosal tissues of pig intestines or bovine lungs. Microsynth was
inquired by an industrial customer to
develop a sensitive multiplex real-time
PCR assay, which is suitable to quantify
residual traces of pig and cow DNA in
heparin and conduct routine testing on
heparin samples. Since heparin is known
to be a strong inhibitor in PCR/real-time
PCR assays, a major challenge of the project was to develop a robust protocol,
which includes the specific digestion of
heparin.
SOP
Documentation
marker. The control marker is used in
combination with an artificial template
and is added to each heparin sample.
Hereby, it is possible to verify the effectiveness of the heparin digest in each
sample and rule out any false-negative
results. In a second phase, heparin samples were analyzed using SOPs that had
been established during the initial setup and validation phase. Finally, the data
was analyzed and reported to the customer.
Customer Benefits
• Microsynth defines and realizes a thorough qPCR strategy for cost-effective
detection of porcine and bovine traces
in heparin samples.
• All from one single source: DNA isolation, multiplex qPCR assay development, production and validation as
well as routine testing.
• Microsynth completed the project in
time and in accordance to the budget
guidelines.
G
43
H
Terms and Conditions
Pricing
• All prices indicated on our Websites,
within our price lists list or within offers do not include VAT or other taxes.
Please make sure that you consider any
taxes within your calculation.
• Payment terms are net 30 days in CHF,
EUR or USD
• Invoices will be issued in Swiss Francs
within Switzerland, EUR within European countries and USD in all other
countries
• When ordering oligonucleotides, our
online shop will already show you a
price calculation. Please be aware that
in rare cases, the webshop quotations
may be higher than the quotations
on your invoice. Quotations on your
invoice will always be calculated according to the current price list and any
general or specific discount you have
been provided.
• Pre-payment may be an elegant way
to facilitate your administrative work
and simultaneously benefit from a significant discount. Please contact us for
further details.
• Should your order be based on a specific offer, please do not forget to men-
H
44
tion your offer number when you will
be asked for. Only thereby it is guaranteed that any provided discount will be
considered when invoicing you.
• Shipping fees can be seen in the actual
price list
Canceling or Revising Your Purchase
Order
In order to deliver the ordered commodity or service as fast as possible, your order will be processed soon after your order submission. Therefore, canceling or
changing your order is only possible for
a very limited time following order submission. In case you would like to cancel or revise your order, please phone
us immediately under the following
numbers:
+49-551 370 00 10 (for Germany)
+41-71-722 83 33 (for Austria, Switzerland and other countries). Just writing
an e-mail may not be sufficient. Note
that beyond usual working hours or
during the weekend and holidays, orders cannot be cancelled or revised. If
order processing has already been started (e.g. your oligo is being synthesized)
it is not possible to cancel or revise the
order. We will deliver the requested commodity/service and invoice you accordingly.
Satisfaction Guarantee
• Microsynth and Seqlab are committed
to offer you the best possible quality.
However, if you should once not be
satisfied please report the problem to
us within three months after receipt
of the product. After 3 months complaints are no longer accepted.
• It is necessary that you provide the production number (or sequence number)
of the product in order to facilitate a
quick handling of your complaint.
• Products sent or billed due to an error
by us will be replaced or reimbursed.
• Products sent or billed due to an error
by the customer will not be replaced or
credited for.
• Please note that Microsynth or Seqlab
cannot be held liable for delivery problems outside our area of control (our
production facility). For instance, any
delivery problems caused by the delivery carrier must be addressed with the
carrier directly.
Products Usage
All products are for research purposes only.
They may not be used for commercial, clinical
diagnostic or any other use. All products are
for use by the purchaser only. The re-sale or
distribution of these products or any product
derived from the use of these products to any
third party is prohibited, unless you have a
special agreement with Microsynth. Especially
excluded is the commercial use or re-sale of
oligonucleotides or other products labeled
with the listed modifiers, which Microsynth is
producing and selling under license of the respective IP owners. Separate licenses for other
than the aforementioned internal R&D application may be available. Please inquire at the
respective IP owner.
License Statements and Trademarks
•ATTO™ Dyes are registered trademarks of
ATTO Technology Inc.
•Alexa Fluor® and Texas Red® are registered
trademarks of Molecular Probes, Inc. Re-
spectively labeled oligonucleotides are produced and sold under license of Molecular
Probes Inc. They are for research use only
and are covered by pending and issued patents.
•Black Hole Quencher™, BHQ-1™ and BHQ2™ are registered trademarks of Biosearch
Technologies, Inc. The BHQ technology is
licensed and sold under agreement with
Biosearch and these products are sold exclusively for R&D use by the purchaser. They
may not be used for clinical or diagnostic
purposes and they may not be re-sold, distributed or re-packaged.
•
C-5 Propynes are covered by patents or
patents pending owned by Isis Pharmaceuticals, Inc. (“Isis”). Purchase of oligos containing C-5 Propynes from Microsynth requires
signing of a notification letter to accept that
such products can be used the solely for internal research.
•Cy3®, Cy5®, Cy5.5® and Cy7®, are registered
trademarks of GE Healthcare.
•
Digoxigenin is sold under licence from
Roche Diagnostics.
•Dyomics™ is a registered trademark of Dyomics GmbH.
•FAM™, HEX™, ROX™, TAMRA™ and TET™ are
trademarks of Applied Biosystems, Inc.
•PowerPlex® 16HS is a registered trademark
of Promega Corporation.
•Yakima Yellow is a registered trademark of
Epoch Biosciences, Inc. Oligonucleotides
labeled with Yakima Yellow are for research
purposes only, and may not be used for
commercial, clinical, diagnostic or any other
use. Such oligonucleotides are subject to
proprietary rights of Epoch Biosciences, Inc.
and are made and sold under license from
Epoch Biosciences, Inc. For commercial use
of such oligonucleotides a license must be
obtained directly from Epoch Biosciences,
Inc.
CONTACT
Germany
Seqlab GmbH
Microsynth AG
Hannah - Vogt - Strasse 1
37085 Göttingen
Germany
Phone: + 49 -551- 370 00 10
E-mail: [email protected]
Web: www.seqlab.de
Postfach 3351
88115 Lindau
Germany
P.O. Box only!
( Only ship by German Post, other
shipping services are not accepted. )
Austria
Microsynth Austria GmbH
Microsynth AG
Leberstrasse 20
1110 Wien
Austria
Web: www.microsynth.at
Postfach 58
6961 Wolfurt-Bahnhof
Austria
P.O. Box only! ( Only ship by Austrian Post,
other shipping services are not accepted. )
Switzerland
Microsynth AG
Headquarter
Schützenstrasse 15
P.O. Box
9436 Balgach
Switzerland
Phone: + 41 71 722 83 33
Fax: + 41 71 722 87 58
Web: www.microsynth.ch
Other Microsynth websites:
www.vaterschafts-test.ch
( only German language )
STS 429
DNA Sanger
Sequencing
Paternity Testing
Certification according to ISO 9001:2008
Accreditation according to EN ISO 17025:2005
printed climateneutrally
Certificate Number:
53196-1312-1005
123-12345-1234-1234
www.climatepartner.com

F - Genoks

Transcription

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