Molecular modelling study of DNA-Troeger's bases interactions

J Biomol Struct Dyn. 1994 Dec;12(3):637-53. doi: 10.1080/07391102.1994.10508764.

Abstract

The two enantiomeric forms: 1R,5R (R) and 1S,5S (S) of the Troeger's base analog, 9,19-methano-9,10,19,20-tetrahydrodiacridino-[b,f]-[1,5]- diazocine which possess a C2 axis of symmetry, are susceptible to interact differently with DNA. This paper reports the results of molecular modelling calculations on B DNA-Troeger's base complexes. Two interaction modes have been examined: intercalation and binding in the grooves. Into the limits of accuracy of such a kind of calculations, some tendencies seem to appear. In the intercalation mode, the R and S enantiomers exhibit a selectivity for alternating dinucleotidic sequences and the minor groove is enantioselective for S. Binding in the major groove is selective for S with G-C sequences, and in the minor groove the stereoselectivity appears for R with A-T sequences. The S-(dG-dC)5.(dG-dC)5 complex in the major groove seems to be the most favoured.

MeSH terms

  • Azocines / chemistry
  • Azocines / metabolism*
  • Base Sequence
  • Computer Graphics
  • Computer Simulation*
  • DNA / chemistry
  • DNA / metabolism*
  • Intercalating Agents / chemistry
  • Intercalating Agents / metabolism
  • Ligands
  • Models, Molecular*
  • Nucleic Acid Conformation*
  • Poly dA-dT / metabolism
  • Polydeoxyribonucleotides / metabolism
  • Software
  • Stereoisomerism

Substances

  • Azocines
  • Intercalating Agents
  • Ligands
  • Polydeoxyribonucleotides
  • Poly dA-dT
  • poly(dC-dG)
  • Troeger's base
  • DNA