title: Mesoscopic modeling for nucleic acid chain dynamics.
abstract: To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model a single-stranded nucleic as a polymer chain whose monomers are the nucleosides. Each monomer comprises a bead representing the sugar molecule and a pin representing the base. The bead-pin complex can rotate about the backbone of the chain. We consider pairwise stacking and hydrogen-bonding interactions. We use a modified Monte Carlo dynamics that splits the dynamics into translational bead motion and rotational pin motion. By performing a number of tests, we first show that our model is physically sound. We then focus on a study of the kinetics of a DNA hairpin--a single-stranded molecule comprising two complementary segments joined by a noncomplementary loop--studied experimentally. We find that results from our simulations agree with experimental observations, demonstrating that our model is a suitable tool for the investigation of the hybridization of single strands.
authors.affiliation: Department Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
authors.forename: M
authors.initials: M
authors.lastname: Sales-Pardo
authors.forename: R
authors.initials: R
authors.lastname: Guimerà
authors.forename: A A
authors.initials: AA
authors.lastname: Moreira
authors.forename: J
authors.initials: J
authors.lastname: Widom
authors.forename: L A N
authors.initials: LA
authors.lastname: Amaral
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000032:analysis / Q000737:chemistry*; D017403:In Situ Hybridization / Q000379:methods*; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000032:analysis / Q000737:chemistry*; D012313:RNA / Q000032:analysis / Q000737:chemistry*; D013329:Structure-Activity Relationship
chemical_list: D009711:Nucleotides; D012313:RNA; D004247:DNA