Cargando…

The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry

Coarse-grained models of DNA have made important contributions to the determination of the physical properties of genomic DNA, working as a molecular machine for gene regulation. In this study, to analyze the global dynamics of long DNA sequences with consideration of sequence-dependent geometry, we...

Descripción completa

Detalles Bibliográficos
Autores principales: Kameda, Takeru, Isami, Shuhei, Togashi, Yuichi, Nishimori, Hiraku, Sakamoto, Naoaki, Awazu, Akinori
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5361685/
https://www.ncbi.nlm.nih.gov/pubmed/28382002
http://dx.doi.org/10.3389/fphys.2017.00103
_version_ 1782516814753824768
author Kameda, Takeru
Isami, Shuhei
Togashi, Yuichi
Nishimori, Hiraku
Sakamoto, Naoaki
Awazu, Akinori
author_facet Kameda, Takeru
Isami, Shuhei
Togashi, Yuichi
Nishimori, Hiraku
Sakamoto, Naoaki
Awazu, Akinori
author_sort Kameda, Takeru
collection PubMed
description Coarse-grained models of DNA have made important contributions to the determination of the physical properties of genomic DNA, working as a molecular machine for gene regulation. In this study, to analyze the global dynamics of long DNA sequences with consideration of sequence-dependent geometry, we propose elastic network models of DNA where each particle represents k nucleotides (1-particle-per-k-nucleotides, 1PkN). The models were adjusted according to profiles of the anisotropic fluctuations obtained from our previous 1-particle-per-1-nucleotide (1P1N) model, which was proven to reproduce such profiles of all-atom models. We confirmed that the 1P3N and 1P4N models are suitable for the analysis of detailed dynamics such as local twisting motion. The models are intended for the analysis of large structures, e.g., 10-nm fibers in the nucleus, and nucleoids of mitochondrial or phage DNA at low computational costs. As an example, we surveyed the physical characteristics of the whole mitochondrial human and Plasmodium falciparum genomes.
format Online
Article
Text
id pubmed-5361685
institution National Center for Biotechnology Information
language English
publishDate 2017
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-53616852017-04-05 The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry Kameda, Takeru Isami, Shuhei Togashi, Yuichi Nishimori, Hiraku Sakamoto, Naoaki Awazu, Akinori Front Physiol Physiology Coarse-grained models of DNA have made important contributions to the determination of the physical properties of genomic DNA, working as a molecular machine for gene regulation. In this study, to analyze the global dynamics of long DNA sequences with consideration of sequence-dependent geometry, we propose elastic network models of DNA where each particle represents k nucleotides (1-particle-per-k-nucleotides, 1PkN). The models were adjusted according to profiles of the anisotropic fluctuations obtained from our previous 1-particle-per-1-nucleotide (1P1N) model, which was proven to reproduce such profiles of all-atom models. We confirmed that the 1P3N and 1P4N models are suitable for the analysis of detailed dynamics such as local twisting motion. The models are intended for the analysis of large structures, e.g., 10-nm fibers in the nucleus, and nucleoids of mitochondrial or phage DNA at low computational costs. As an example, we surveyed the physical characteristics of the whole mitochondrial human and Plasmodium falciparum genomes. Frontiers Media S.A. 2017-03-14 /pmc/articles/PMC5361685/ /pubmed/28382002 http://dx.doi.org/10.3389/fphys.2017.00103 Text en Copyright © 2017 Kameda, Isami, Togashi, Nishimori, Sakamoto and Awazu. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Physiology
Kameda, Takeru
Isami, Shuhei
Togashi, Yuichi
Nishimori, Hiraku
Sakamoto, Naoaki
Awazu, Akinori
The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry
title The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry
title_full The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry
title_fullStr The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry
title_full_unstemmed The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry
title_short The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry
title_sort 1-particle-per-k-nucleotides (1pkn) elastic network model of dna dynamics with sequence-dependent geometry
topic Physiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5361685/
https://www.ncbi.nlm.nih.gov/pubmed/28382002
http://dx.doi.org/10.3389/fphys.2017.00103
work_keys_str_mv AT kamedatakeru the1particleperknucleotides1pknelasticnetworkmodelofdnadynamicswithsequencedependentgeometry
AT isamishuhei the1particleperknucleotides1pknelasticnetworkmodelofdnadynamicswithsequencedependentgeometry
AT togashiyuichi the1particleperknucleotides1pknelasticnetworkmodelofdnadynamicswithsequencedependentgeometry
AT nishimorihiraku the1particleperknucleotides1pknelasticnetworkmodelofdnadynamicswithsequencedependentgeometry
AT sakamotonaoaki the1particleperknucleotides1pknelasticnetworkmodelofdnadynamicswithsequencedependentgeometry
AT awazuakinori the1particleperknucleotides1pknelasticnetworkmodelofdnadynamicswithsequencedependentgeometry
AT kamedatakeru 1particleperknucleotides1pknelasticnetworkmodelofdnadynamicswithsequencedependentgeometry
AT isamishuhei 1particleperknucleotides1pknelasticnetworkmodelofdnadynamicswithsequencedependentgeometry
AT togashiyuichi 1particleperknucleotides1pknelasticnetworkmodelofdnadynamicswithsequencedependentgeometry
AT nishimorihiraku 1particleperknucleotides1pknelasticnetworkmodelofdnadynamicswithsequencedependentgeometry
AT sakamotonaoaki 1particleperknucleotides1pknelasticnetworkmodelofdnadynamicswithsequencedependentgeometry
AT awazuakinori 1particleperknucleotides1pknelasticnetworkmodelofdnadynamicswithsequencedependentgeometry