Sanghani S R, Lavery R
Laboratoire de Biochimie Théorique, CNRS URA 77, Institut de Biologie Physico-Chimique, Paris, France.
Nucleic Acids Res. 1994 Apr 25;22(8):1444-9. doi: 10.1093/nar/22.8.1444.
Molecular modelling has been used to probe the conformational 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 (alpha:gamma, g-/g(+)-->t/t) or to the alpha beta gamma-flip form proposed from fibre studies (alpha:beta:gamma, g-/t/g(+)-->t/g+/t). The latter transition is also found to be linked to BI-->BII transitions (epsilon:zeta, t/g(-)-->g-/t).
分子建模已被用于探究双链DNA-RNA杂交体的构象偏好。正如所预期的那样，DNA链的糖具有更高的构象灵活性，但是，对于所研究的大多数重复序列而言，这些糖更倾向于C2-内向型构象，而核糖糖则一致采用C3-内向型构象。这导致了一种强烈的异源双链构象。该规则的一个例外涉及聚（dT）·聚（rA）的胸腺嘧啶链，其略微倾向于C3-内向型构象。我们的研究进一步表明，杂交体的DNA链更倾向于经典B结构域中的主链扭转，而不是基于纤维衍射研究提出的修正值。然而，主链构象转变仍可被诱导，导致αγ翻转（α:γ，g-/g(+)-->t/t）或纤维研究提出的αβγ翻转形式（α:β:γ，g-/t/g(+)-->t/g+/t）。还发现后一种转变与BI-->BII转变（ε:ζ，t/g(-)-->g-/t）有关。
