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.

Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments / S. Di Leo, S. Marni, C.A. Plata, T.P. Fraccia, G.P. Smith, A. Maritan, S. Suweis, T. Bellini. - In: PLOS COMPUTATIONAL BIOLOGY. - ISSN 1553-734X. - 18:4(2022), pp. e1010051.1-e1010051.20. [10.1371/journal.pcbi.1010051]

Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments

S. Di Leo;S. Marni;T.P. Fraccia;T. Bellini
2022

Abstract

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.
Nucleic Acid Conformation; Nucleic Acid Hybridization; Solutions; Temperature; Thermodynamics; DNA
Settore FIS/07 - Fisica Applicata(Beni Culturali, Ambientali, Biol.e Medicin)
PRIN201718TBELL_01 - SOFT ADAPTIVE NETWORKS - BELLINI, TOMMASO GIOVANNI - PRIN2017 - PRIN bando 2017 - 2018
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/943746
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