A possible family of B-like triple helix structures: comparison with the Arnott A-like triple helix

Biochemistry. 1993 Mar 2;32(8):2098-103. doi: 10.1021/bi00059a030.

Abstract

Recent experimental studies of the structure of triple helices show that their conformation in solution differs from the A-like structure derived from diffraction data on triple helix fibers by Arnott and co-workers. Here we show by means of molecular modeling that a family of triple helix structures may exist with similar conformational energies, but with a variety of sugar puckers. The characteristics of these putative triple helices are analyzed for three different base sequences: (T.AxT)n, (C.GxC+)n, and alternating (C.GxC+/T.AxT)n. In the case of (C.GxC+)n triple helix, infrared and Raman spectra have been obtained and clearly reveal the existence of both N- and S-type sugars in solution. The molecular mechanics calculations allow us to propose a stereochemically reasonable model for this triple helix, in good agreement with the vibrational spectroscopy results.

Publication types

  • Comparative Study

MeSH terms

  • Algorithms
  • Base Composition
  • DNA / chemistry*
  • Macromolecular Substances
  • Nucleic Acid Conformation*
  • Polydeoxyribonucleotides / chemistry*
  • Software
  • Structure-Activity Relationship

Substances

  • Macromolecular Substances
  • Polydeoxyribonucleotides
  • DNA