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Consequences of primer binding-sites polymorphisms on genotyping practice

Author(s): Estefânia M. Martins | Laura Vilarinho | Sofia Esteves | Mónica Lopes-Marques | António Amorim | Luísa Azevedo

Journal: Open Journal of Genetics
ISSN 2162-4453

Volume: 01;
Issue: 02;
Start page: 15;
Date: 2011;
Original page

Keywords: Primer Binding-site | SNP | &lt | i&gt | PAH&lt | /i&gt | Gene | Molecular Genetics

Herein we investigated the effect of primer binding site polymorphisms in achieving correct genotyping when a mismatch occurs in distinct positions of the primer sequence. For that purpose primer sequences were designed in order to carry either allelic form at the 3’ end and at 3 bp, 5 bp and 7 bp apart from the 3’ end of an intronic polymorphism (rs2247836) observed in phenylalanine hydroxylase (PAH) gene. For one of the alleles annealing failure was obtained when the mismatch occurs at all the four primer-site locations. Primer sequences carrying the alternative SNP allele resulted to be less specific as the distance to the primer-3’ end was increased. Altogether, these results revealthat effects in the extension of the annealing failure is allele and mismatch-position dependent.

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