DNA structure and polymerase fidelity: A new role for A-DNA

Although the recent structural studies on polymerases have brought new insi ghts on polymerase fidelity, the role of DNA sequence and structure is not well understood. Here, the analysis of the crystal structures of hotspots f or polymerase slippage shows that, in the B-form, these sequences share com mon structural alterations which may explain the high rate of replication e rrors. In (CA)(n) tracts, a "Janus-like" structure with shifted base pairs in the major groove but an apparent normal geometry in the minor groove con stitutes a molecular decoy which can mislead the polymerases. A model of th e rat polymerase beta bound to this structure suggests that an altered conf ormation of the nascent template-primer duplex can interfere with correct n ucleotide incorporation by affecting the geometry of the active site and br eaking the rules of base pairing while at the same time escaping enzymatic mechanisms of error discrimination scanning for the correct geometry of the minor groove. In contrast, by showing that the A-form greatly attenuates t he sequence-dependent structural alterations in hotspots, this study reveal s that the A-conformation of the nascent template-primer duplex at the vici nity of the polymerase active site will contribute to fidelity. The A-form may play the role of a structural buffer which preserves the correct geomet ry of the active site for all sequences. The comparison of the conformation of the nascent template-primer duplex in five available crystal structures of DNA polymerase-DNA complexes shows indeed that polymerase beta, the lea st accurate enzyme, is unique in binding to a B-DNA duplex even close to it s active site. This model leads to several predictions which are discussed in the light of published experimental data.