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Nucleic Acids Research, 1994, Vol. 22, No. 8 1444-1449
© 1994

STRUCTURAL BIOLOGY

Theoretical studies of DNA-RNA hybrid conformations

Sanjay R. Sanghani and Richard Lavery*

Laboratoire de Biochimie Theorique, CNRS URA 77, Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie, Paris 75005, France

*To whom correspondence should be addressed

Received December 20, 1993. Revised March 21, 1994. Accepted March 21, 1994.

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 {alpha}:{gamma}-flip (a:y, g-/g+ - t/t) or to the {alpha}ß{gamma}-flip form proposed from fibre studies ({alpha}:ß:{gamma}, g->/t/g+ - t/g*plus;/t). The latter transition is also found to be linked to BI -> BII transitions ({varepsilon}:{zeta}, t/g- -> g-/t).


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