Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments.
Journal
PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922
Informations de publication
Date de publication:
04 2022
04 2022
Historique:
received:
19
01
2022
accepted:
22
03
2022
revised:
21
04
2022
pubmed:
12
4
2022
medline:
26
4
2022
entrez:
11
4
2022
Statut:
epublish
Résumé
Understanding of the pairing statistics in solutions populated by a large number of distinct solute species with mutual interactions is a challenging topic, relevant in modeling the complexity of real biological systems. Here we describe, both experimentally and theoretically, the formation of duplexes in a solution of random-sequence DNA (rsDNA) oligomers of length L = 8, 12, 20 nucleotides. rsDNA solutions are formed by 4L distinct molecular species, leading to a variety of pairing motifs that depend on sequence complementarity and range from strongly bound, fully paired defectless helices to weakly interacting mismatched duplexes. Experiments and theory coherently combine revealing a hybridization statistics characterized by a prevalence of partially defected duplexes, with a distribution of type and number of pairing errors that depends on temperature. We find that despite the enormous multitude of inter-strand interactions, defectless duplexes are formed, involving a fraction up to 15% of the rsDNA chains at the lowest temperatures. Experiments and theory are limited here to equilibrium conditions.
Identifiants
pubmed: 35404933
doi: 10.1371/journal.pcbi.1010051
pii: PCOMPBIOL-D-22-00089
pmc: PMC9022813
doi:
Substances chimiques
Solutions
0
DNA
9007-49-2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1010051Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Annu Rev Biophys Biomol Struct. 2004;33:415-40
pubmed: 15139820
Nat Commun. 2015 Mar 10;6:6424
pubmed: 25752840
Nucleic Acids Res. 2019 Apr 23;47(7):3284-3294
pubmed: 30753582
Biopolymers. 2011 Jul;95(7):472-86
pubmed: 21384337
Curr Opin Struct Biol. 2015 Feb;30:1-6
pubmed: 25464122
Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1110-5
pubmed: 22233803
ACS Nano. 2016 Sep 27;10(9):8508-16
pubmed: 27571250
Phys Life Rev. 2018 Aug;25:1-21
pubmed: 29170011
Science. 2007 Nov 23;318(5854):1276-9
pubmed: 18033877
Biopolymers. 1997;44(3):217-39
pubmed: 9591477
Biochemistry. 2004 Mar 30;43(12):3537-54
pubmed: 15035624
J Am Chem Soc. 2017 Mar 1;139(8):3134-3144
pubmed: 28191938
Biophys J. 2013 Aug 6;105(3):756-66
pubmed: 23931323
Nucleic Acids Res. 2002 Nov 1;30(21):e122
pubmed: 12409481
J Comput Chem. 2011 Jan 15;32(1):170-3
pubmed: 20645303
Biophys J. 2017 Feb 28;112(4):565-567
pubmed: 28256216
Phys Rev E. 2021 Apr;103(4-1):042503
pubmed: 34005886
Science. 1995 Jul 21;269(5222):364-70
pubmed: 7618102
Biophys Chem. 2005 Oct 3;117(3):207-15
pubmed: 15963627
ACS Nano. 2018 Oct 23;12(10):9750-9762
pubmed: 30280566
Curr Opin Struct Biol. 2001 Feb;11(1):114-9
pubmed: 11179900
Biophys J. 2017 Feb 28;112(4):683-691
pubmed: 28256228
Science. 1993 Sep 10;261(5127):1411-8
pubmed: 7690155
Science. 2019 Feb 22;363(6429):884-887
pubmed: 30792304
Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6190-5
pubmed: 16606839
Proc Natl Acad Sci U S A. 2021 Feb 23;118(8):
pubmed: 33593911