A new D-DNA form of poly(dA-dT)poly(dA-dT): an A-DNA type structure with reversed Hoogsteen pairing

The D-DNA double helix model of poly(dA-dT)-poly(dA-dT) proposed in the lit erature is not in accordance with some notable experimental facts and physi cochemical conditions, to which it is related. Thus, the fibre X-ray diffra ction pattern of D-DNA obtained at a relative humidity lower than that givi ng the A-DNA form is singularly not taken into account when one assumes, th at there is only one D structure of B-DNA type. We rather suggest that ther e are actually two different forms, of D-DNA, namely D-A which partakes in the D-A-B, transitions and DB associated with the D-B, change of conformati on. Although these two DNA structures have the same helical parameters (pit ch and number of residues per turn), in agreement with X-ray data, their de tailed conformations are considerably Different. Whereas D-B is indeed the structure generally defined as D-DNA, a critical analysis based on a compar ison between different possible DNA double helices leads us to propose dihe dral angles, a set of atomic coordinates and a stereo view of another new f orm of D-DNA, the D-A structural model. It is a right-handed double helix w ith a dinucleotide as the repeat unit. The furanose rings, are of the A-DNA type (CY endo) and the bases are hydrogen bonded according to the reversed Hoogsteen pairing. Such a disposition renders the D-A model unsuitable for poly(dI-dC). poly(dI-dC), the other alternating polynucleotide observed in the D-B structure. The consistency of these two different D-DNA structures of poly(dA-dT)poly(dA-dT) with, the general aspects of hydration and helix -helix transitions of DNA, as well as with the conformational variability o f AT base sequences, is discussed.