Cooperativity-Dependent Folding of Single-Stranded DNA

The folding of biological macromolecules is a fundamental process of which we lack a full comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming nonspecific secondary structures that are difficult to characterize with b...

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Autores principales:	X. Viader-Godoy, C. R. Pulido, B. Ibarra, M. Manosas, F. Ritort
Formato:	article
Lenguaje:	EN
Publicado:	American Physical Society 2021
Materias:	Physics QC1-999
Acceso en línea:	https://doaj.org/article/50446c0ce7224f209a1053867f16390e
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spelling	oai:doaj.org-article:50446c0ce7224f209a1053867f16390e2021-12-02T19:06:49ZCooperativity-Dependent Folding of Single-Stranded DNA10.1103/PhysRevX.11.0310372160-3308https://doaj.org/article/50446c0ce7224f209a1053867f16390e2021-08-01T00:00:00Zhttp://doi.org/10.1103/PhysRevX.11.031037http://doi.org/10.1103/PhysRevX.11.031037https://doaj.org/toc/2160-3308The folding of biological macromolecules is a fundamental process of which we lack a full comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming nonspecific secondary structures that are difficult to characterize with biophysical techniques. Here, we present a helix-coil model for secondary-structure formation, where ssDNA bases are organized in two different types of domains (compact and free). The model contains two parameters: the energy gain per base in a compact domain, ε, and the cooperativity related to the interfacial energy between different domains, γ. We test the ability of the model to quantify the formation of secondary structure in ssDNA molecules mechanically stretched with optical tweezers. The model reproduces the experimental force-extension curves in ssDNA of different molecular lengths and varying sodium and magnesium concentrations. Salt-correction effects for the energy of compact domains and the interfacial energy are found to be compatible with those of DNA hybridization. The model also predicts the folding free energy and the average size of domains at zero force, finding good agreement with secondary-structure predictions by mfold. We envision the model could be further extended to investigate native folding in RNA and proteins.X. Viader-GodoyC. R. PulidoB. IbarraM. ManosasF. RitortAmerican Physical SocietyarticlePhysicsQC1-999ENPhysical Review X, Vol 11, Iss 3, p 031037 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Physics QC1-999
spellingShingle	Physics QC1-999 X. Viader-Godoy C. R. Pulido B. Ibarra M. Manosas F. Ritort Cooperativity-Dependent Folding of Single-Stranded DNA
description	The folding of biological macromolecules is a fundamental process of which we lack a full comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming nonspecific secondary structures that are difficult to characterize with biophysical techniques. Here, we present a helix-coil model for secondary-structure formation, where ssDNA bases are organized in two different types of domains (compact and free). The model contains two parameters: the energy gain per base in a compact domain, ε, and the cooperativity related to the interfacial energy between different domains, γ. We test the ability of the model to quantify the formation of secondary structure in ssDNA molecules mechanically stretched with optical tweezers. The model reproduces the experimental force-extension curves in ssDNA of different molecular lengths and varying sodium and magnesium concentrations. Salt-correction effects for the energy of compact domains and the interfacial energy are found to be compatible with those of DNA hybridization. The model also predicts the folding free energy and the average size of domains at zero force, finding good agreement with secondary-structure predictions by mfold. We envision the model could be further extended to investigate native folding in RNA and proteins.
format	article
author	X. Viader-Godoy C. R. Pulido B. Ibarra M. Manosas F. Ritort
author_facet	X. Viader-Godoy C. R. Pulido B. Ibarra M. Manosas F. Ritort
author_sort	X. Viader-Godoy
title	Cooperativity-Dependent Folding of Single-Stranded DNA
title_short	Cooperativity-Dependent Folding of Single-Stranded DNA
title_full	Cooperativity-Dependent Folding of Single-Stranded DNA
title_fullStr	Cooperativity-Dependent Folding of Single-Stranded DNA
title_full_unstemmed	Cooperativity-Dependent Folding of Single-Stranded DNA
title_sort	cooperativity-dependent folding of single-stranded dna
publisher	American Physical Society
publishDate	2021
url	https://doaj.org/article/50446c0ce7224f209a1053867f16390e
work_keys_str_mv	AT xviadergodoy cooperativitydependentfoldingofsinglestrandeddna AT crpulido cooperativitydependentfoldingofsinglestrandeddna AT bibarra cooperativitydependentfoldingofsinglestrandeddna AT mmanosas cooperativitydependentfoldingofsinglestrandeddna AT fritort cooperativitydependentfoldingofsinglestrandeddna
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Cooperativity-Dependent Folding of Single-Stranded DNA

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