Thermodynamic evaluation of the impact of DNA mismatches in PCR-type SARS-CoV-2 primers and probes.

ABSTRACT:

Background

DNA mismatches can affect the efficiency of PCR techniques if the intended target has mismatches in primer or probe regions. The accepted rule is that mismatches are detrimental as they reduce the hybridization temperatures, yet a more quantitative assessment is rarely performed.

Methods

We calculate the hybridization temperatures of primer/probe sets after aligning to SARS-CoV-2, SARS-CoV-1 and non-SARS genomes, considering all possible combinations of single, double and triple consecutive mismatches. We consider the mismatched hybridization temperature within a range of 5 ^∘C to the fully matched reference temperature.

Results

We obtained the alignments of 19 PCR primers sets that were recently reported for the detection of SARS-CoV-2 and to 216

SUBMITTER: Miranda P 

PROVIDER: S-EPMC7888997 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature