hello every body, I want to design the normal primer for cdns sequence. This sequence has a snp t / c. How to design a primer and which one of the t or c alleles? how? Someone can help? thanks.
T or C is designated as Y in ambiguity codes. Simply put a 'Y' in your sequence when you order the oligo . When the oligo is made you will get an equimolar mixture of T containing and C containing oligos so whatever the base present in your amplimer your oligos will amplify all the sequences present
T or C is designated as Y in ambiguity codes. Simply put a 'Y' in your sequence when you order the oligo . When the oligo is made you will get an equimolar mixture of T containing and C containing oligos so whatever the base present in your amplimer your oligos will amplify all the sequences present
Please check this paper, I hope it helps !
https://www.sciencedirect.com/science/article/abs/pii/S0731708516305593
Hi Shokoofeh
you can also use ARMS-PCR for which you do an a multiplex PCR, an amplicon used for PCR control used in the two tubes, and separately by tube one primer couple (one of them harboring the "T") and the second couple (harboring the "C"). take a look at that (http://grcpk.com/wp-content/uploads/2014/10/7.-ARMS.pdf).
fred
Which version of the sequence do you want? If you want both, simply design primers that flank the SNP, clone into a plasmid, sequence 5-6 colonies and you should be able to obtain both variants.
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