Identification and analysis of a template-primer (ds-DNA) binding cleft in E. coli DNA polymerase I: an electrostatic...

In the modeled structure of the Klenow fragment of E. coli DNA polymerase I, we have identified a distinct region that exhibits a strong electropositive potential contour. The examination of the distribution of the electropositive and negative potential across the two-dimensional slices of the modeled structure revealed that the positive potential was concentrated around the cleft. The approximate size and shape of the region appears well suited to accommodate eight base pairs of duplex DNA and is consistent with the position of the dsDNA binding cleft reported in the crystal structure [Beese et al., Science (1993) 260, 352-355].