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Transient kinetics measured with force steps discriminate between double-stranded DNA elongation and melting and define the reaction energetics

Under a tension of ∼65 pN, double-stranded DNA undergoes an overstretching transition from its basic (B-form) conformation to a 1.7 times longer conformation whose nature is only recently starting to be understood. Here we provide a structural and thermodynamic characterization of the transition by...

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Autores principales: Bongini, Lorenzo, Melli, Luca, Lombardi, Vincenzo, Bianco, Pasquale
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950695/
https://www.ncbi.nlm.nih.gov/pubmed/24353317
http://dx.doi.org/10.1093/nar/gkt1297
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author Bongini, Lorenzo
Melli, Luca
Lombardi, Vincenzo
Bianco, Pasquale
author_facet Bongini, Lorenzo
Melli, Luca
Lombardi, Vincenzo
Bianco, Pasquale
author_sort Bongini, Lorenzo
collection PubMed
description Under a tension of ∼65 pN, double-stranded DNA undergoes an overstretching transition from its basic (B-form) conformation to a 1.7 times longer conformation whose nature is only recently starting to be understood. Here we provide a structural and thermodynamic characterization of the transition by recording the length transient following force steps imposed on the λ-phage DNA with different melting degrees and temperatures (10–25°C). The shortening transient following a 20–35 pN force drop from the overstretching force shows a sequence of fast shortenings of double-stranded extended (S-form) segments and pauses owing to reannealing of melted segments. The lengthening transients following a 2–35 pN stretch to the overstretching force show the kinetics of a two-state reaction and indicate that the whole 70% extension is a B-S transition that precedes and is independent of melting. The temperature dependence of the lengthening transient shows that the entropic contribution to the B-S transition is one-third of the entropy change of thermal melting, reinforcing the evidence for a double-stranded S-form that maintains a significant fraction of the interstrand bonds. The cooperativity of the unitary elongation (22 bp) is independent of temperature, suggesting that structural factors, such as the nucleic acid sequence, control the transition.
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spelling pubmed-39506952014-03-12 Transient kinetics measured with force steps discriminate between double-stranded DNA elongation and melting and define the reaction energetics Bongini, Lorenzo Melli, Luca Lombardi, Vincenzo Bianco, Pasquale Nucleic Acids Res Under a tension of ∼65 pN, double-stranded DNA undergoes an overstretching transition from its basic (B-form) conformation to a 1.7 times longer conformation whose nature is only recently starting to be understood. Here we provide a structural and thermodynamic characterization of the transition by recording the length transient following force steps imposed on the λ-phage DNA with different melting degrees and temperatures (10–25°C). The shortening transient following a 20–35 pN force drop from the overstretching force shows a sequence of fast shortenings of double-stranded extended (S-form) segments and pauses owing to reannealing of melted segments. The lengthening transients following a 2–35 pN stretch to the overstretching force show the kinetics of a two-state reaction and indicate that the whole 70% extension is a B-S transition that precedes and is independent of melting. The temperature dependence of the lengthening transient shows that the entropic contribution to the B-S transition is one-third of the entropy change of thermal melting, reinforcing the evidence for a double-stranded S-form that maintains a significant fraction of the interstrand bonds. The cooperativity of the unitary elongation (22 bp) is independent of temperature, suggesting that structural factors, such as the nucleic acid sequence, control the transition. Oxford University Press 2014-03 2013-12-17 /pmc/articles/PMC3950695/ /pubmed/24353317 http://dx.doi.org/10.1093/nar/gkt1297 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Bongini, Lorenzo
Melli, Luca
Lombardi, Vincenzo
Bianco, Pasquale
Transient kinetics measured with force steps discriminate between double-stranded DNA elongation and melting and define the reaction energetics
title Transient kinetics measured with force steps discriminate between double-stranded DNA elongation and melting and define the reaction energetics
title_full Transient kinetics measured with force steps discriminate between double-stranded DNA elongation and melting and define the reaction energetics
title_fullStr Transient kinetics measured with force steps discriminate between double-stranded DNA elongation and melting and define the reaction energetics
title_full_unstemmed Transient kinetics measured with force steps discriminate between double-stranded DNA elongation and melting and define the reaction energetics
title_short Transient kinetics measured with force steps discriminate between double-stranded DNA elongation and melting and define the reaction energetics
title_sort transient kinetics measured with force steps discriminate between double-stranded dna elongation and melting and define the reaction energetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950695/
https://www.ncbi.nlm.nih.gov/pubmed/24353317
http://dx.doi.org/10.1093/nar/gkt1297
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