Helix-helix transitions in DNA: fibre X-ray study of the particular cases poly(dG-dC). poly(dG-dC) and poly(dA). 2poly(dT).

Abstract

The helix-helix transitions which occur in poly(dG-dC). poly(dG-dC) and in poly (dG-m(5)dC). poly(dG-m(5)dC) are commonly assumed to be changes between the right-handed A- or B-DNA double helices and the left-handed Z-DNA structure. The mechanisms for such transconformations are highly improbable, especially when they are supposed to be active in long polynucleotide chains organised in semicrystalline fibres. The present alternative possibility assumes that rather than the Z-DNA it is a right-handed double helix (S-DNA) which actually takes part in these form transitions. Two molecular models of this S form, in good agreement with X-ray measurements, are proposed. They present alternating C(2')-endo and C(3')-endo sugar puckering like the "alternating B-DNA" put forward some years ago. Dihedral angles, sets of atomic coordinates and stereo views of the two S-DNA structures are given, together with curves of calculated diffracted intensities. Furthermore, we question the possibility of obtaining semicrystalline fibres with triple helices of poly(dA). 2poly(dT) in a way which renders X-ray diffraction efficient. It is suggested that, up to now, only double helices of poly(dA). poly(dT) can actually be observed by fibre X-ray diffraction measurements.