FESTIVE CLOSURE

Festive Closure

The service will close down over the festive period. We aim to process any sequencing samples arriving before or on the first post of Friday 22nd of December. Any sequencing samples arriving after that will be stored and processed on our return (3rd January). For other sample types please contact us.

Resources | Primers | Compatibility with Common Plasmids

Overview

The tables below provide information regarding the compatibility of common sequencing primers with common plasmids. We are unable to provide information on all primers / plasmids in use, so if you do not see the information you need, please check for compatibility yourself.  We have provided some suggestions below on how to go about checking primer compatibility.  

In the tables below, "tick" indicates that the priming site is present. "cross" indicates that, to the best of our knowledge, the priming site is not present.

 

Common Cloning Vectors

Vector Manufacturer PRIMER
T7 T3 M13F M13R KS SP6 T7 Terminator
pBluescript I & II Stratagene tick tick tick tick tick cross cross
pPCR Script Stratagene tick tick cross tick tick cross cross
pCR2.1 ,-XL, -Blunt Life Technologies  tick cross tick tick cross cross cross
pCR-II, pCR-Blunt-II Life Technologies tick cross tick tick cross tick cross
pGEM-1, 9Zf Promega tick cross cross cross cross tick* cross
pGEM-3Z; -3,5,7,11,13Zf Promega tick cross cross cross cross tick cross
pGEM-4Z Promega tick cross tick tick cross tick* cross
pGEM-T, -T Easy Promega tick cross tick tick cross tick cross
pT7T3 GE Healthcare  tick tick cross cross cross cross cross
Lambda Zap Stratagene tick tick tick tick tick cross cross

* There is a 4 bp mismatch at the 5' end of the priming sequence in this vector.

 

GST Fusion Vectors

Vector Manufacturer PRIMER
pGEXF pGEXR pEBG2T Rev
pGEX-1, pGEX-1lT GE Healthcare  tick tick cross
pGEX-2T, pGEX-2TK GE Healthcare  tick tick cross
pGEX-3X GE Healthcare  tick tick cross
pGEX-4T1, -4T2, -4T3 GE Healthcare  tick tick cross
pGEX-5X1, -5X2, -5X3 GE Healthcare  tick tick cross
pGEX-6P1, -6P2, -6P3 GE Healthcare  tick tick cross
pEBG-2T N/A tick cross tick

 

T7 Promoter Vectors

Vector Manufacturer PRIMER
T7 T7 Terminator
pET (all known) Merck Millipore  tick tick

 

Baculovirus Expression Vectors

Vector Manufacturer PRIMER
pFastBacForward pFastBac Reverse
pFastBac-1 Life Technologies tick tick
pFastBac-HTa, -HTb, -HTc Life Technologies tick tick

 

Mammalian Expression Vectors

Vector Manufacturer PRIMER
CMVF CMVR T7 SP6
pCDNA3 Life Technologies  tick N/A tick tick*
pCMV5 N/A tick tick N/A N/A

* The "T" residue at base 4 of the new SP6 primer is not present in the pCDNA3 SP6 priming site.

 

Establishing Plasmid / Primer Compatibility

Assessment of primer compatibility with standard, well-characterised cloning plasmids can be done by comparing the primer sequence against the known sequence of one's plasmid of interest. If you intend on using any of our standard primers, we would still recommend checking that the sequence is actually the same by examining the tables above.

If you do not have immediate access to detailed plasmid information, identifying the plasmid source via the company page or a simple google search may help. Most commercial suppliers will have detailed information (often including the full sequence) for their plasmids on their websites. They will also usually provide information on which standard primers work with their plasmids or provide the sequence of custom primers that can be utilised for sequencing reactions.  If you are unable to identify the optimal primer to use by examining the plasmid map, we recommend downloading the sequence and opening the file using a DNA manipulation program. You can then align different primers to the sequence and see which ones align and where they are, relative to your cloning site.

If your plasmid is not a commercially available one, there are several next steps you can try:

  1. Request the sequence from the individual who supplied the plasmids
  2. Perform sequencing reactions with a few standard plasmids in the hopes of returning appropriate sequence
  3. Use an internal primer within the insert to sequence out into the plasmid. This step assumes that you may know some of the sequence is or should be. Once you have this sequence, you can check to see if any standard priming sites are present or design your own primer.

Do you need any help? Please get in touch and we’ll be happy to lend a hand.