title: An extension of the rigorous base-unit oriented description of nucleic acid structures.
abstract: Our proposed description for DNA base/base-pair structures (1), though rigorous, does not satisfy some of the requirements as established at the Cambridge Workshop (2). Here, we propose a revised description for base/base-unit structures of nucleic acids. This new description is as rigorous and satisfies all the requirements (2). Following the original approach, the moment-of-inertia frame is still the choice of the internal coordinate system for a base/base-unit. The revised description has the minimum number of parameters (i.e., six parameters per rigid body) in the set. Besides regular Watson-Crick type of helices (e.g., A-DNA, A-RNA, B-DNA, Z-DNA, etc.), the revised description also works for non-Watson-Crick, multiple stranded molecules (e.g., triplex, quadruplex, etc.) as well as parallel stranded molecules.
authors.affiliation: Theoretical Biology and Biophysics (T-10), Theoretical Division, Los Alamos National Laboratory, NM 87545.
authors.forename: C S
authors.initials: CS
authors.lastname: Tung
authors.forename: D M
authors.initials: DM
authors.lastname: Soumpasis
authors.forename: G
authors.initials: G
authors.lastname: Hummer
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011089:Polydeoxyribonucleotides / Q000737:chemistry
chemical_list: D011089:Polydeoxyribonucleotides; C051802:triplex DNA; D004247:DNA