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, "" indicates that the priming site is present. "" 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
pPCR Script	Stratagene
pCR2.1 ,-XL, -Blunt	Life Technologies
pCR-II, pCR-Blunt-II	Life Technologies
pGEM-1, 9Zf	Promega						*
pGEM-3Z; -3,5,7,11,13Zf	Promega
pGEM-4Z	Promega						*
pGEM-T, -T Easy	Promega
pT7T3	GE Healthcare
Lambda Zap	Stratagene

* 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
pGEX-2T, pGEX-2TK	GE Healthcare
pGEX-3X	GE Healthcare
pGEX-4T1, -4T2, -4T3	GE Healthcare
pGEX-5X1, -5X2, -5X3	GE Healthcare
pGEX-6P1, -6P2, -6P3	GE Healthcare
pEBG-2T	N/A

T7 Promoter Vectors

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

Baculovirus Expression Vectors

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

Mammalian Expression Vectors

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