Abstract

The interaction energies between (Ala)₁₀ and α-helix fragment and different nucleotide sequences in right-handed B-form have been optimized using semi-empirical potential energy functions. The energies are calculated for two different orientations of the α-helix, viz., when the αhelix axis taken in the N→C direction is (i) parallel and (ii) antiparallel to the 5′-3′ ascending strand of DNA proximal to it. When both the DNA molecule as well as the ?-helix are treated as rigid molecules it is found that a polyalanine α-helix has slightly more favourable contacts when it is in the proximity of a four nucleotide sequence of 5′-(N-A-T-N)-3′ type, where N is either a purine or a pyrimidine. However, when the two interacting molecules are allowed to undergo local structural variations then the interaction energy appears to be independent of the base sequence confirming the non-specific nature of these interactions.