Primers are an integral part of all sequencing reactions and facilitate the acquisition of sequence information 3’ of their binding site. Many primers are commonly found within numerous plasmids in routine use throughout the molecular biology realm. DNA Sequencing and Services have identified many of these in order to assist customers with their sequencing needs.
Below is a table of all the primers that we provide free of charge to all our customers.
| Primer Name | Primer Sequence (5'->3') | Plasmid Specificity |
Comments |
|---|---|---|---|
| SK | TCTAGAACTAGTGGATC | ||
| KS | TCGAGGTCGACGGTAT | ||
| CMV F | CGCAAATGGGCGGTAGGCGTG | At 5' end of MCS in pCMV5 (4) | This is a "Universal" primer and should work in any vector that contains a CMV promoter. However, as with any primer, customers should still check for compatibility with their plasmid. |
| CMV R | CCTCCACCCCATAATATTATAGAAGGACAC | At 3' end of MCS in pCMV5 | |
| M13 F | GTAAAACGACGGCCAGTG | Common to many plasmids (-20 version) | This primer does NOT work with Invitrogen Gateway vectors (e.g. pDONR221) due to a base mismatch at the 3' end. Our primer contains a "G" at the extreme 3' end, but the Gateway plasmids possess a "C" at this position. For sequencing Gateway vectors, please use the Gateway-specific primers we have. |
| M13 F(GW) | TGTAAAACGACGGCCAGT | Specific for Gateway vectors | |
| M13 R | GGAAACAGCTATGACCATG | Common to many plasmids | There is a base deletion in some pUC18 vectors that results in the M13Rev primer not binding. Details of this deletion can be found in the New England Biolabs catalogue (p136 of the 2003 catalogue). If you use pUC18 you may wish to use a different primer in case your plasmid is affected. |
| M13 R(GW) | CAGGAAACAGCTATGACC | Specific for Gateway vectors | |
| SP6 | AGCTATTTAGGTGACACTATAG | Common to many plasmids | Many plasmids diverge outside the core SP6 promoter sequence. If you plan to use the SP6 primer, you MUST check your plasmid sequence to ensure the primer is compatible. |
| T3 | AATTAACCCTCACTAAAGGG | Common to many plasmids | |
| T7 | TAATACGACTCACTATAGGG | Common to many plasmids | |
| T7 Term | TATGCTAGTTATTGCTCAG | Common to many plasmids | |
| Bac F | TATTCCGGATTATTCATACCGTC | At 5' end of MCS in pFastBac-1 | |
| Bac R | CAACAATTGCATTCATTTTATGTTTCAGG | ||
| Bac R (old) | GTATGGCTGATTATGATCCTC | At 3' end of MCS in pFastBac-1 | |
| BGH R | TAGAAGGCACAGTCGAGG | For mammalian expression vectors (8) | For sequencing from the 3' end of mammalian expression vectors containing the BGH polyadenylation signal. |
| DuetDOWN1 | GATTATGCGGCCGTGTACAA | For pETDuet, pACYCDuet vectors (7) | These primers work in the Duet vectors for co-expression of proteins. DuetDOWN1 gives a reverse read of T7 transcription start-1 MCS. DuetUP2 gives a forward read of T7 transcription start-2 MCS. |
| DuetUP2 | TTGTACACGGCCGCATAATC | For pETDuet, pACYCDuet vectors (7) | These primers work in the Duet vectors for co-expression of proteins. DuetDOWN1 gives a reverse read of T7 transcription start-1 MCS. DuetUP2 gives a forward read of T7 transcription start-2 MCS. |
| GAL4AD | AATACCACTACAATGGATGATGTAT | For Y2H library vectors (5) | These primers are for yeast two hybrid bait and library vectors. Due to the increasing number of Y2H systems available, customers are advised to check their particular Y2H vectors to ensure that the primers will work before they ask us to use these primers. |
| GAL4BD | TCATCGGAAGAGAGTAGTAACAAAG | For Y2H bait vectors (5) | These primers are for yeast two hybrid bait and library vectors. Due to the increasing number of Y2H systems available, customers are advised to check their particular Y2H vectors to ensure that the primers will work before they ask us to use these primers. |
| Mal F | GGTCGTCAGACTGTCGATGAAGCC | Present in plasmids such as: pMALp2x,pMal4CE | |
| Mal R | AATCTTATCTCATCCGCCAAAACAGCCAAG | Present in plasmids such as: plasmids pMALp2x,pMal4CE | |
| p10 F | CCTTTAATTCAACCCAACACAATATATTATAGTTAAATAAGAATTATTAT | For pFBDual vector | |
| p10 R | CAAACGACCCAACACCCGTGCG | For pFBDual vector | |
| pACT F | GGATGATGTATATAACTATCTATTCGATGATGAAGATAC | For pACT2 Y2H vector | |
| pACT R | GGCAAAACGATGTATAAATGAAAGAAATTGAGATGG | For pACT2 Y2H vector | |
| pAS F | CTGATATGCCTCTAACATTGAGACAGCATAG | For pAS2-1 Y2H vector | |
| pAS R | AATAAGAGCGACCTCATGCTATACCTGAG | For pAS2-1 Y2H vector | |
| pBABE F | CCTCCTCTTCTTCCATCC | For pBABE puro, pBABE neo vectors | |
| pBABE R | CCACACCTGGTTGCTGACTAATTGAG | For pBABE puro, pBABE neo vectors | |
| pcDNA5 R | CACCTACTCAGACAATGCGATGCAA | For pcDNA5- and pcDNA3-based plasmids | |
| pEGFP-C1 | CATGGTCCTGCTGGAGTTCGTGAC | For pEGFPC1/2/3 vector | |
| pEGFP-Cter | CCATTATAAGCTGCAATAAACAAGTTAACAACAACAATTG | For pEGFPC1/2/3 vector | |
| pEGFP-N1R | GGCCGTTTACGTCGCCGTCC | For pEGFP-N1 vector | |
| pET Upstream | ATGCGTCCGGCGTAGA | For pETDuet, pACYCDuet vectors (7) | These primers work in the Duet vectors for co-expression of proteins. DuetDOWN1 gives a reverse read of T7 transcription start-1 MCS. DuetUP2 gives a forward read of T7 transcription start-2 MCS. |
| pGEX F | CCAGCAAGTATATAGCATGG | Common to pGEX plasmids | |
| pGEX R | CCGGGAGCTGCATGTGTCAGAGG | Common to pGEX plasmids | |
| pLEXA-C-F | TTTCTGCACAATATTTCAAGC | For pLEXA-C bait vector (6) | These primers are for the Dualsystems DUALhybrid yeast two hybrid pLEXA-C bait vector. Note that these primers are not compatible with the pLEXA-N bait vector or the pGAD-HA library vector (however, the GAL4AD primer we have should work for the pGAD-HA vector). |
| pLEXA-C-R | ATGAGATCAAACACCTCTTG | For pLEXA-C bait vector (6) | These primers are for the Dualsystems DUALhybrid yeast two hybrid pLEXA-C bait vector. Note that these primers are not compatible with the pLEXA-N bait vector or the pGAD-HA library vector (however, the GAL4AD primer we have should work for the pGAD-HA vector). |
| pmCherryC1-F | GTTGGACATCACCTCCCACAACGAG | For pmCherry-C1 vector (9) | For sequencing mCherry vectors. mCherry-C1-Fwd sequences from within the 3' end of the Cherry ORF and into the MCS (C-terminal fusion vector). mCherry-N1-Rev sequences back into the MCS from the 5' end of the ORF (N-terminal fusion vector). |
| pmCherryN1-R | GGGGCGGCCCTCGCCCTCGCCCTCG | For pmCherry-N1 vector (9) | For sequencing mCherry vectors. mCherry-C1-Fwd sequences from within the 3' end of the Cherry ORF and into the MCS (C-terminal fusion vector). mCherry-N1-Rev sequences back into the MCS from the 5' end of the ORF (N-terminal fusion vector). |
| LKO.1 | GACTATCATATGCTTACCGT | Human U6 promoter 5' | For sequencing inserts in plasmids that use the U6 promotor to synthesise short shRNA, siRNA, gDNA (CRISPR), etc sequences. Check that your plasmid is compatible! |
The list provided is under constant review so customers can feel free to suggest additional primers that may be useful. Our staff will review these suggestions. Please note that any new additions to the list of primers will take into consideration those that will be most widely used by the research community at large.
Special Considerations
As a reminder, our various standard primers indicated above, are available to customers free of charge!
Please note that when selecting any of our standard primers, it is critical to check that they are compatible with your template! Additional details regarding compatibility with commonly used vectors for molecular biology and biochemistry can be found on our Compatibility with Common Plasmids page.