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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2017
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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 |
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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 |
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