Theoretical studies of DNA-RNA hybrid conformations

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Abstract
Molecular modelling has been used to probe the con-formational preferences of double stranded DNA-RNA hybrids. As might be expected, the sugars of the DNA strand have higher conformational flexibility, but, for the majority of the repetitive sequences studied, these sugars prefer a C2′-endo pucker, while ribose sugars uniformly adopt a C3′-endo pucker. This gives rise to a strongly heteronomous duplex conformation. One exception to this rule involves the thymidine strand of poly(dT).poly(rA), which marginally prefers a C3-endo pucker. Our study further indicates that the DNA strands of the hybrids favour backbone torsions in the canonical B domain, rather than the modified values proposed on the basis of fibre diffraction studies. Backbone conformational transitions can nevertheless be induced leading to an α:γ-flip (a:y, g-/g+ - t/t) or to the αβγ-flip form proposed from fibre studies (α:β:γ, g→/t/g+ - t/g*plus;/t). The latter transition is also found to be linked to BI → BII transitions (ε:ζ, t/g- → g-/t).