Measuring the geometry of DNA grooves

Biopolymers. 1994 Mar;34(3):337-46. doi: 10.1002/bip.360340305.

Abstract

We present a new method for measuring the widths and depths of the grooves formed within DNA helices. This method overcomes the limitations of simply measuring interstrand phosphate-phosphate distances and has the advantage of yielding continuous values for groove geometry along a DNA fragment. In the case of oligonucleotides, it also clearly indicates the zones in which grooves exist, bounded by two phosphodiester backbones. The methodology has been developed within the Curves algorithm for studying irregular DNA geometries and is based on the optimal, and generally curved, helical axis obtained by this analysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Base Sequence
  • Crystallography
  • DNA / chemistry*
  • Molecular Sequence Data
  • Molecular Structure
  • Nucleic Acid Conformation

Substances

  • DNA