The impact of abasic sites on DNA flexibility

We use internal coordinate molecular mechanics calculations to study the im pact of abasic sites on the conformation and the mechanics of the DNA doubl e helix. Abasic sites, which are common mutagenic lesions, are shown to loc ally modify both the groove geometry and the curvature of DNA in a sequence dependent manner. By controlled twisting and bending, it is also shown tha t these lesions modify the deformability of the duplex, generally increasin g its flexibility, but again to an extent which depends on the nature of th e abasic site and on the surrounding base sequence. Both the conformational and mechanical influence of this type of DNA damage may be significant for recognition and repair mechanisms.