An extension of the rigorous base-unit oriented description of nucleic acid structures

J Biomol Struct Dyn. 1994 Jun;11(6):1327-44. doi: 10.1080/07391102.1994.10508071.

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Composition
  • Base Sequence
  • Computer Simulation*
  • DNA / chemistry*
  • Models, Molecular*
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Polydeoxyribonucleotides / chemistry

Substances

  • Polydeoxyribonucleotides
  • triplex DNA
  • DNA