Cargando…

Bubble Relaxation Dynamics in Homopolymer DNA Sequences

Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard–Bishop–Dauxois model of DNA to st...

Descripción completa

Detalles Bibliográficos
Autores principales: Hillebrand, Malcolm, Kalosakas, George, Bishop, Alan R., Skokos, Charalampos
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9920605/
https://www.ncbi.nlm.nih.gov/pubmed/36770707
http://dx.doi.org/10.3390/molecules28031041
_version_ 1784887111366737920
author Hillebrand, Malcolm
Kalosakas, George
Bishop, Alan R.
Skokos, Charalampos
author_facet Hillebrand, Malcolm
Kalosakas, George
Bishop, Alan R.
Skokos, Charalampos
author_sort Hillebrand, Malcolm
collection PubMed
description Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard–Bishop–Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine–thymine (AT) and guanine–cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule’s dynamics, for times between 0.5–500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule.
format Online
Article
Text
id pubmed-9920605
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-99206052023-02-12 Bubble Relaxation Dynamics in Homopolymer DNA Sequences Hillebrand, Malcolm Kalosakas, George Bishop, Alan R. Skokos, Charalampos Molecules Article Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard–Bishop–Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine–thymine (AT) and guanine–cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule’s dynamics, for times between 0.5–500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule. MDPI 2023-01-20 /pmc/articles/PMC9920605/ /pubmed/36770707 http://dx.doi.org/10.3390/molecules28031041 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Hillebrand, Malcolm
Kalosakas, George
Bishop, Alan R.
Skokos, Charalampos
Bubble Relaxation Dynamics in Homopolymer DNA Sequences
title Bubble Relaxation Dynamics in Homopolymer DNA Sequences
title_full Bubble Relaxation Dynamics in Homopolymer DNA Sequences
title_fullStr Bubble Relaxation Dynamics in Homopolymer DNA Sequences
title_full_unstemmed Bubble Relaxation Dynamics in Homopolymer DNA Sequences
title_short Bubble Relaxation Dynamics in Homopolymer DNA Sequences
title_sort bubble relaxation dynamics in homopolymer dna sequences
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9920605/
https://www.ncbi.nlm.nih.gov/pubmed/36770707
http://dx.doi.org/10.3390/molecules28031041
work_keys_str_mv AT hillebrandmalcolm bubblerelaxationdynamicsinhomopolymerdnasequences
AT kalosakasgeorge bubblerelaxationdynamicsinhomopolymerdnasequences
AT bishopalanr bubblerelaxationdynamicsinhomopolymerdnasequences
AT skokoscharalampos bubblerelaxationdynamicsinhomopolymerdnasequences