title: Development of coarse-graining DNA models for single-nucleotide resolution analysis.
abstract: Recently, analytical techniques have been developed for detecting single-nucleotide polymorphisms in DNA sequences. Improvements of the sequence identification techniques has attracted much attention in several fields. However, there are many things that have not been clarified about DNA. In the present study, we have developed a coarse-graining DNA model with single-nucleotide resolution, in which potential functions for hydrogen bonds and the pi-stack effect are taken into account. Using Langevin-dynamics simulations, several characteristics of the coarse-grained DNA have been clarified. The validity of the present model has been confirmed, compared with other experimental and computational results. In particular, the melting temperature and persistence length are in good agreement with the experimental results for a wide range of salt concentrations.
authors.affiliation: Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, Japan. doi@me.es.osaka-u.ac.jp
authors.forename: Kentaro
authors.initials: K
authors.lastname: Doi
authors.forename: Tomoaki
authors.initials: T
authors.lastname: Haga
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Shintaku
authors.forename: Satoyuki
authors.initials: S
authors.lastname: Kawano
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods*; D008956:Models, Chemical; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000737:chemistry / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D009711:Nucleotides; D004247:DNA