PRIMEval: Optimization and screening of multiplex oligonucleotide assays.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
17 12 2019
17 12 2019
Historique:
received:
28
06
2019
accepted:
03
12
2019
entrez:
19
12
2019
pubmed:
19
12
2019
medline:
6
11
2020
Statut:
epublish
Résumé
The development of multiplex polymerase chain reaction and microarray assays is challenging due to primer dimer formation, unspecific hybridization events, the generation of unspecific by-products, primer depletion, and thus lower amplification efficiencies. We have developed a software workflow with three underlying algorithms that differ in their use case and specificity, allowing the complete in silico evaluation of such assays on user-derived data sets. We experimentally evaluated the method for the prediction of oligonucleotide hybridization events including resulting products and probes, self-dimers, cross-dimers and hairpins at different experimental conditions. The developed method allows explaining the observed artefacts through in silico WGS data and thermodynamic predictions. PRIMEval is available publicly at https://primeval.ait.ac.at.
Identifiants
pubmed: 31848453
doi: 10.1038/s41598-019-55883-4
pii: 10.1038/s41598-019-55883-4
pmc: PMC6917790
doi:
Substances chimiques
DNA Primers
0
Oligonucleotide Probes
0
Oligonucleotides
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
19286Références
Annu Rev Biophys Biomol Struct. 2004;33:415-40
pubmed: 15139820
Biotechniques. 1995 Jan;18(1):84-6, 88-90
pubmed: 7702859
Bioinformatics. 2009 Jun 1;25(11):1422-3
pubmed: 19304878
Genome Biol. 2009;10(3):R25
pubmed: 19261174
Mol Cell Probes. 2004 Dec;18(6):369-72
pubmed: 15488375
Clin Microbiol Rev. 2018 Feb 28;31(2):
pubmed: 29490932
Nat Struct Mol Biol. 2012 May 13;19(6):623-7
pubmed: 22580558
Genomics. 2017 Jul;109(3-4):312-319
pubmed: 28502701
Bioinformatics. 2005 Dec 15;21(24):4363-70
pubmed: 16234322
BMC Bioinformatics. 2012 Jun 18;13:134
pubmed: 22708584
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Nucleic Acids Res. 2008 Jun;36(11):e66
pubmed: 18492719
Nucleic Acids Res. 2018 Jul 2;46(W1):W252-W256
pubmed: 29718464
J Mol Diagn. 2014 Mar;16(2):163-73
pubmed: 24370857
Methods Mol Biol. 2007;402:3-34
pubmed: 17951788
Methods Mol Biol. 2015;1275:201-13
pubmed: 25697662
Methods Mol Biol. 1993;15:31-40
pubmed: 21400260
Nucleic Acids Res. 2012 Aug;40(15):e115
pubmed: 22730293
Nat Biotechnol. 2019 Feb;37(2):152-159
pubmed: 30718882
Nucleic Acids Res. 1990 Feb 25;18(4):999-1005
pubmed: 2179874
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712