Thermodynamic evaluation of the impact of DNA mismatches in PCR-type SARS-CoV-2 primers and probes.
Mol Cell Probes
; 56: 101707, 2021 04.
Article
in English
| MEDLINE | ID: covidwho-1087137
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
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 21665 SARS-CoV-2 genomes as well as 323 genomes of other viruses of the coronavirus family of which 10 are SARS-CoV-1. We find that many incompletely aligned primers become fully aligned to most of the SARS-CoV-2 when mismatches are considered. However, we also found that many cross-align to SARS-CoV-1 and non-SARS genomes.CONCLUSIONS:
Some primer/probe sets only align substantially to most SARS-CoV-2 genomes if mismatches are taken into account. Unfortunately, by the same mechanism, almost 75% of these sets also align to some SARS-CoV-1 and non-SARS viruses. It is therefore recommended to consider mismatch hybridization for the design of primers whenever possible, especially to avoid undesired cross-reactivity.Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
DNA, Viral
/
DNA Probes
/
Polymerase Chain Reaction
/
DNA Primers
/
Base Pair Mismatch
/
SARS-CoV-2
/
Nucleic Acid Hybridization
Type of study:
Experimental Studies
/
Randomized controlled trials
Language:
English
Journal:
Mol Cell Probes
Journal subject:
Molecular Biology
/
Biotechnology
Year:
2021
Document Type:
Article
Affiliation country:
J.mcp.2021.101707
Similar
MEDLINE
...
LILACS
LIS