I have a gene in hand. If this gene is divided into four domains, namely A, B, A, and B, the sequences of the two A domains and the two B domains are identical, but the gene of the first B domain has mutated. How can I design primers that do not bind to the second B domain?
DEar Zhangrui Tang
the dpmains are identical in terms of AA sequence or DNA?
A possible solution, if your gene is not too big, is ask for the sintesis of a codon optimized gene those use for the repeated domains different codons, in this way you will be able to desing specific primers to insert a mutation selectivelly in one of the 2 repeated sequences.
best regards
Manuele
How big is the change? Are you talking one SNP, a few SNPS, VNTR, InDel?
Got to be specific if you want specific help.
Put one primer so the 3' end has as much of the divergent sequence as possible in Gene B and put the other primer in a flanking region.
Or using tetraARMS PCR
Or dCAPs primers/other variation of enzyme-digest
Or just amplify the whole darn thing & Sanger sequence.
- Badges
- Science topic