Deoxyribonucleic acid (DNA) hybridization is at the heart of countless biological and biotechnological processes. Its theoretical modeling played a crucial role, since it has enabled extracting the relevant thermodynamic parameters from systematic measurements of DNA melting curves. In this article, we propose a framework based on statistical physics to describe DNA hybridization and melting in an arbitrary mixture of DNA strands. In particular, we are able to analytically derive closed expressions of the system partition functions for any number N of strings and explicitly calculate them in two paradigmatic situations: (i) a system made of self-complementary sequences and (ii) a system comprising two mutually complementary sequences. We derive the melting curve in the thermodynamic limit (N→∞) of our description, which provides a full justification for the extra entropic contribution that in classic hybridization modeling was required to correctly describe within the same framework the melting of sequences either self-complementary or not. We thus provide a thorough study comprising limit cases and alternative approaches showing how our framework can give a comprehensive view of hybridization and melting phenomena.

Statistical physics of DNA hybridization / C.A. Plata, S. Marni, A. Maritan, T. Bellini, S. Suweis. - In: PHYSICAL REVIEW. E. - ISSN 2470-0045. - 103:4(2021 Apr 19), pp. 042503.1-042503.10. [10.1103/PhysRevE.103.042503]

Statistical physics of DNA hybridization

S. Marni
Secondo
;
T. Bellini
Penultimo
;
2021

Abstract

Deoxyribonucleic acid (DNA) hybridization is at the heart of countless biological and biotechnological processes. Its theoretical modeling played a crucial role, since it has enabled extracting the relevant thermodynamic parameters from systematic measurements of DNA melting curves. In this article, we propose a framework based on statistical physics to describe DNA hybridization and melting in an arbitrary mixture of DNA strands. In particular, we are able to analytically derive closed expressions of the system partition functions for any number N of strings and explicitly calculate them in two paradigmatic situations: (i) a system made of self-complementary sequences and (ii) a system comprising two mutually complementary sequences. We derive the melting curve in the thermodynamic limit (N→∞) of our description, which provides a full justification for the extra entropic contribution that in classic hybridization modeling was required to correctly describe within the same framework the melting of sequences either self-complementary or not. We thus provide a thorough study comprising limit cases and alternative approaches showing how our framework can give a comprehensive view of hybridization and melting phenomena.
Base Sequence; Models, Theoretical; Thermodynamics; Nucleic Acid Hybridization
Settore FIS/07 - Fisica Applicata(Beni Culturali, Ambientali, Biol.e Medicin)
19-apr-2021
Article (author)
File in questo prodotto:
File Dimensione Formato  
PhysRevE.103.042503.pdf

accesso riservato

Tipologia: Publisher's version/PDF
Dimensione 592.26 kB
Formato Adobe PDF
592.26 kB Adobe PDF   Visualizza/Apri   Richiedi una copia
Pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/916175
Citazioni
  • ???jsp.display-item.citation.pmc??? 2
  • Scopus 5
  • ???jsp.display-item.citation.isi??? 4
social impact