title: A duplex DNA model with regular inter-base-pair hydrogen bonds.
abstract: It is well known that base-pair stacking is the main factor in stabilizing DNA duplex and plays an important role in determining DNA sequence-dependence. What is the dominant force in base-pair stacking? This fundamental biological question remains a challenging problem. Here, based on recent studies about the non-planarity of amino groups on DNA bases, we propose a new duplex DNA model, in which all base amino groups are non-planar and participate in forming regular inter-base-pair hydrogen bonds (IBP H-bonds). This model implies that IBP H-bonds are the dominant force stabilizing base-pair stacking and play a crucial role in determining the geometry and physical properties of sequence-dependent twisted stacking between adjacent base pairs. The model presents a new insight into the link, through regular IBP H-bonds, between base-sequence, fine structure and physical properties at dinucleotide step level, and provides an attractively concise, uniform and quantitative interpretation for various experimentally observed DNA sequence-dependent properties in terms of regular IBP H-bonds. It would provide a new approach to understanding the dynamics and underlying mechanisms of DNA sequence-dependent biological processes, sequence-structure-property relationships, DNA strand separation during replication and transcriptions, etc.
authors.affiliation: Department of Biomedical Engineering, Kunming University of Science and Technology, Kunming 650051, China. lxq@public.km.yn.cn
authors.forename: Xu-Qing
authors.initials: XQ
authors.lastname: Li
authors.forename: Ping
authors.initials: P
authors.lastname: Fan
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D006860:Hydrogen Bonding; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA