AUTHOR=Kameda Takeru , Isami Shuhei , Togashi Yuichi , Nishimori Hiraku , Sakamoto Naoaki , Awazu Akinori TITLE=The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry JOURNAL=Frontiers in Physiology VOLUME=8 YEAR=2017 URL=https://www.frontiersin.org/journals/physiology/articles/10.3389/fphys.2017.00103 DOI=10.3389/fphys.2017.00103 ISSN=1664-042X ABSTRACT=

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.