Structure of the alpha-form of poly[d(A)].poly[d(T)] and related polynucleotide duplexes

The alpha-form of polyd(A)].polyd(T)], observed in fibers at high (greater than 80%) relative humidity, is a 10-fold double-helical structure of pitch 3.2 nm. This new X-ray analysis shows that the two strands of the double helix are of the same kind conformationally and both B-like in containing C-2'-endo-puckered deoxyribose rings. Nevertheless, the two strands are different enough for the overall morphology of the duplex to resemble that of the heteromerous model for the drier (beta) form of polyd(A)].polyd(T)] in which one strand has C-2'-endo rings and the other C-3'-endo. Since the orientations of the bases in polyd(A)].polyd(T)] are persistently different from those of classical B-DNA it is likely that there will be local bending (about 10 degrees) at the junctions between general sequence tracts and the oligod(A)].oligod(T)] tracts that occur in some native DNAs. The conclusions about the structure of alpha-polyd(A)].polyd(T)] are reinforced by independent analyses of similar X-ray diffraction patterns from polyd(A)].polyd(U)] and polyd(A-I)].polyd(C-T)].