Pre-designed PCR/Sanger sequencing primer pairs

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Pre-designed PCR/Sanger sequencing primer pairs
PRODUCT BULLETIN
Primer Designer
™
Pre-designed PCR/Sanger sequencing primer pairs
Find the primer pair you need with Primer Designer tool
™
Introduction
Primer Designer is a free online tool to search for the right PCR/Sanger
primer pair from a database of >300,000 pre-designed primer pairs for
resequencing the human exome. The tool also provides a streamlined
ordering process, allowing you to directly purchase primer pairs online.
Depending on the specific application and desired workflow, primers can
be ordered unmodified, M13-tailed, HPLC-purified, or desalted.
70% Benefits
• Complete primer design for all of the human exome
• Find primers in seconds with the user-friendly interface—search
by genome position, gene symbol, SNP identifier, and other genome
annotations
• Primers are designed to be free of SNPs and primer-dimers, highly
target-specific, and used under universal PCR conditions
• Visualized map view for the primer pair on the Primer Designer tool
• Primer pairs are selected to tile across exons for optimal exon
coverage with a minimal number of primer pairs
• Fully automated online ordering—including primer search and primer
configuration
• All primers are quality checked by mass spectrometry
• 192 primer pairs selected from top cancer genes are tested by
Life Technologies
™
Optimal performance
In order to provide the best primers for optimal performance, we have
utilized our proprietary algorithm to help ensure that (1) all primers are
free of common SNPs listed in dbSNP build 135, (2) primer-dimers are
avoided, (3) primer specificity is high (no off-target hybridization; primer
pair is specific to the target region), and (4) universal PCR conditions can
be used.
The average amplicon size among the >300,000 primer pairs is designed
to be around 500 bp, so that a typical exon can be amplified with only one
primer pair (Figure 1).
Distribution of amplicon (%)
™
60% 50% 40% 30% 20% 10% 0% 0-­‐100 101-­‐200 201-­‐300 301-­‐400 401-­‐500 501-­‐600 Amplicon Size Figure 1. Amplicon size of the predesigned primer pairs. Most primer pairs
are designed to amplify around 500 bp,
minimizing the number of primer pairs
needed.
Simple ways to search
Primer Designer tool—the first
online tool to search for PCR/
Sanger sequencing primers any way
you like.
™
A
Search by:
• Target information such as gene,
gene symbol, SNP ID, COSMIC ID,
or RefSeq (multiple target search
is available)
• Sequence in FASTA format
• Chromosome coordinates
• Uploading your next-generation
sequencing results in .vcf format
For all Primer Designer primers,
you can obtain relevant target
information such as PCR amplicon
length, exon number, chromosome
position, and primer sequence
(website log-in required).
™
View primers on a gene map
You can view each primer pair and
PCR amplicon on a gene map built
within the Primer Designer web
tool (Figure 2).
™
B
Figure 2. View primer details and gene maps on the Primer Designer web tool.
An example of primer pairs for the BRAF gene is shown. (A) The View Details
icon provides information like primer sequence (orange arrow), SNP identified
using this primer pair (blue arrow), and access to the map (red arrow). (B) Map
view, which allows you to easily view all primer pairs available and visually select
between primer pairs.
™
Pick your own primer
configuration
Primer Designer is not only a
search tool, but it also provides
automated ordering features to
configure your primer order. You
can add universal M13 tails, select
a purification method (desalted or
HPLC-purified), and place an order
directly online, thereby greatly
simplifying the ordering process
(Figure 3).
™
100% QC by mass spectrometry
All Primer Designer primers
are manufactured at our site in
Pleasanton, CA (ISO 13485 certified)
with automated manufacturing
processes to accommodate high
throughput and for consistency.
All primers are analyzed by mass
spectrometry before shipping
to you. For US and Canadian
customers, the standard turnaround
time for primer orders is 2 business
days (desalted
primers).
™
Figure 3. Primer configuration before ordering. Select M13-tailed or non-tailed primers (see
side bar), desalted or HPLC purification, and order a primer pair or one primer only. Primer pairs
will be delivered in separate tubes after ordering.
Compatible with all BigDye
chemistries
®
The most popular 192 primer pairs,
selected from top cancer genes or
diseases, have been tested with
BigDye Terminator v1.1 and v3.1
chemistry and also with the latest
BigDye Direct Cycle Sequencing
kits. All Primer Designer primers
are compatible with BigDye
sequencing chemistries with a
primer design success rate of >95%.
®
®
™
®
M13-tailed vs. non-tailed primers
Non-tailed primers: Forward and reverse primers are used for both the PCR and
sequencing reactions. Each primer pair is amplicon-specific. If you sequence 10
different products, you have 20 sequencing reactions to prepare with 20 different
primers—this is more complicated, time consuming, and can introduce sources of
error.
M13-tailed primers: M13 (-21) Forward–tailed primers and M13 Reverse–tailed
primers are used for the PCR reaction. M13 (-21) Forward and M13 Reverse primers
are used for the sequencing reaction, independent of the PCR product to sequence. If
you sequence 10 different PCR products, you have 20 sequencing reactions to prepare,
but the forward and reverse reactions each use the same primer (10 reactions with
the M13 (-21) Forward primer and 10 reactions with the M13 Reverse primer). This
is less complicated, requires less preparation time, and minimizes sources of error.
Sequencing primers are available for ordering (Cat. No. A15637 and A15638).
Primer pairs when you need them
Sanger sequencing is the trusted standard for DNA sequencing, proven through decades of results that includes
sequencing of the first human genome. Life Technologies is committed to providing continuing solutions to
streamline the Sanger sequencing workflow. The Primer Designer tool is the next step in that commitment,
providing you with a simple online tool to find and order the primer pairs you need.
™
Ordering information
Cat. No. Full name
Short description
Primer 5’-tail Purification
option
method
Synthesis
Minimal
scale spec yield
A15629 Human, Forward PCR/SEQ primer, desalted
Human, FWD primer, Ds
Non-tailed
Desalted
25 nmole
8 nmole
A15630 Human, Reverse PCR/SEQ primer, desalted
Human, REV primer, Ds
Non-tailed
Desalted
25 nmole
8 nmole
A15631 Human, Forward PCR/SEQ primer, HPLC
Human, FWD primer, HPLC
Non-tailed
HPLC
50 nmole 900 pmole
A15632 Human, Reverse PCR/SEQ primer, HPLC
Human, REV primer, HPLC
Non-tailed
HPLC
50 nmole 900 pmole
A15633 Human, Forward PCR primer, M13-tailed, desalted M13 Human, FWD primer, Ds
M13-tailed
Desalted
25 nmole
8 nmole
A15634 Human, Reverse PCR primer, M13-tailed, desalted M13 Human, REV primer, Ds
M13-tailed
Desalted
25 nmole
8 nmole
A15635 Human, Forward PCR primer, M13-tailed, HPLC
M13 Human, FWD primer, HPLC M13-tailed
HPLC
50 nmole 900 pmole
A15636 Human, Reverse PCR primer, M13-tailed, HPLC
M13 Human, REV primer, HPLC
HPLC
50 nmole 900 pmole
A15637 M13 (-21) Forward sequencing primer
M13 (-21) seq FWD primer, HPLC N/A
HPLC
50 nmole 900 pmole
A15638 M13 Reverse sequencing primer
M13 seq REV primer, HPLC
HPLC
50 nmole 900 pmole
M13-tailed
N/A
Please refer to the Quick Reference Guide for further primer configuration details.
Get started today at lifetechnologies.com/primerdesigner
For Research Use Only. Not for use in diagnostic procedures. © 2013 Life Technologies Corporation. All rights reserved. The trademarks
mentioned herein are the property of Life Technologies Corporation and/or its affiliate(s) or their respective owners. CO34214 0913

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