Geometrical correlations useful for design of sequence-specific DNA narrow groove binding ligands.

Isohelical geometry of sequence-specific DNA narrow groove binding ligands was analyzed in terms of H-bond donor/acceptor complementarity between the base pair atoms facing into the narrow groove and the corresponding H-bond donating atoms regularly disposed along the ligand molecule. Spatial correlations found in analytical form were applied to analysis of naturally occurring and hypothetical drug molecule structures. For the case of B-like isohelices the permitted values of the distance L0 between each two neighboring H-bond donating atoms of the ligand as well as the bending angle tau 0 of the line subsequently connecting these atoms were estimated as follows: L0 congruent to (5.0 +/- 0.4) A; tau 0 congruent to (26 +/- 2) degrees.