For a Taq polymerase reaction, let's say that I have a primer A (which I cannot prevent from being extensible, it has a natural 3' end) which can hybridize to a known point on a synthetic DNA oligonucleotide sequence (B).
Is there a modification I can include in the sequence of B which would prevent A from extending? I thought I could use abasic sites, but from what I'm reading, polymerase will go right over them, filling them in randomly. I also know it can go over a few RNA bases.
Is there anything else that would stop it in its tracks?
Milos, Perhaps a 5'-5' inverted nucleotide on the template strand would cause the Taq pol to stall without incorporating a nucleotide due to a poor fit. Trilink offers oligos with inverted nucleotide as a modification. https://www.trilinkbiotech.com/catalogsearch/result/?q=Inverted
Use a primer with a 3' Phosphate group.
https://secure.eurogentec.com/product/research-lc-hybridization-probes.html
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