A study of H-bonding of 3- and 5-substituted 6-aminouracils in duplex and triplex structures

Nucleosides Nucleotides Nucleic Acids. 2005;24(5-7):907-10. doi: 10.1081/ncn-200059263.

Abstract

All possible dimers of the title modified bases with native nucleobases [10 dimers from 3-methylated 6-aminouracils (3sau) and 20 from 5-methyled 6-aminouracils (5sau), respectively have been calculated by ab initio method (Hartree-Fock method, 3 21G basis set). We have found two potential duplexes of 5sau and three possible duplexes of 3sau. Altogether seven dimers containing one or two bifurcating H-bonds have been found. Later on, five triplexes from ten possible calculated dimers have been found. In two of them the amino group of 6-aminouracil moiety takes part in H-bonding and there are H-bonds, too, between the first and third base of the triplexes causing an extra stabilization.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • DNA / chemistry
  • Dimerization
  • Hydrogen Bonding*
  • Models, Chemical
  • Models, Molecular
  • Molecular Biology / methods*
  • Nucleic Acid Conformation
  • Nucleic Acid Denaturation
  • Nucleic Acid Heteroduplexes*
  • Software
  • Uracil / chemistry*

Substances

  • Nucleic Acid Heteroduplexes
  • Uracil
  • DNA