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.
Highlights
Genomic DNA plays many functional roles such as a medium for the storage of genetic information and as a molecular machine involved in gene expression regulation
For most k values up to k = 15, the profiles of mean square fluctuation (MSF) of the n-th particle (Fna, Fnb, Fns, and Fnt ) and the correlations of fluctuations between the n-th and l-th particles (Fncl) in the 1PkN model were similar to the corresponding values (Gai, Gbi, Gsi, Gti, and Gcij) obtained in the 1P1N model (Figures 4–7; Figures S1–S16)
We developed the 1PkN model, which is more coarse-grained than recent DNA models and is intended for the analysis of the dynamic properties of long DNA molecules
Summary
Genomic DNA plays many functional roles such as a medium for the storage of genetic information and as a molecular machine involved in gene expression regulation. Each nucleoid generally contains negative supercoils of DNA, which notably enhance the transcription and replication of genetic loci (Bogenhagen et al, 2014; Farge et al, 2014; Kukat et al, 2015). This observation indicates that the physical processes involving DNA, such as the formation and deformation of nucleoids, perform important functions in the regulation of gene expression in prokaryotes
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