The synthetic deoxydodecamer d(C-G-C-G-A-A-T-T-A-G-C-G) was analyzed by x-ray
diffraction methods, and the structure was refined to a residual error of R =
0.17 at 2.5-A resolution (2 sigma data) with 83 water molecules located. The
sequence crystallizes as a full turn of a B-DNA helix and contains 2 purine X
purine (G.A) base pairs and 10 Watson-Crick base pairs. The analysis shows
conclusively that adenine is in the syn orientation with respect to the sugar
moiety whereas guanine adopts the usual trans orientation. Nitrogen atoms of
both bases are involved in hydrogen bonding with the N-1 of guanine 2.84 A from
the N-7 of adenine and the N-6 of adenine within 2.74 A of the O-6 of guanine.
The C-1'...C-1' separation is 10.7 A close to that for standard Watson-Crick
base pairs. The incorporation of the purine.purine base pairs at two steps in
the dodecamer causes little perturbation of either the local or the global
conformation of the double helix. Comparison of the structural features with
those of the G.T wobble pair and the standard G.C pair suggests a rationale for
the differential enzymatic repair of the two types of base-pair mismatches.
