Molecular modelling study of DNA-Troeger's bases interactions

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.