Salazar M, Reid B R
Department of Chemistry, University of Washington, Seattle 98195.
J Mol Biol. 1993 Oct 5;233(3):509-23. doi: 10.1006/jmbi.1993.1528.
The solution structure of the DNA:RNA hybrid duplex d(GTCACATG):r(caugugac) has been determined by means of two-dimensional nuclear Overhauser effect (2D-NOE) spectra, restrained molecular dynamics and full-relaxation matrix stimulation of the 2D-NOE spectra. The DNA:RNA hybrid duplex assumes neither an A-form nor a B-form structure in solution, but an intermediate heteromerous duplex structure. The sugars of the RNA strand have a normal N-type C3'-endo conformation, but the DNA strand sugars have neither N-type nor S-type conformations; instead, they have an unexpected intermediate O4'-endo conformation. The negative x-displacement, as well as the small rise and positive inclination of the base-pairs, resembles A-form morphology but the minor groove width is intermediate between that of A-form and B-form duplexes. Both the DNA and RNA strands show prominent sequence-dependent variations in their helical parameters. Combined analysis of NOE and J-coupling data indicates that the DNA sugars are not in a dynamical two-state equilibrium. The detailed three-dimensional structure of this DNA:RNA hybrid molecule leads to a proposed model for its interaction with RNase H. Several specific structural features of the enzyme complexed with the hybrid duplex appear to explain the mechanism whereby RNase H discriminates between DNA:RNA hybrid duplexes and pure RNA:RNA duplexes.
通过二维核Overhauser效应（2D-NOE）光谱、受限分子动力学以及2D-NOE光谱的全弛豫矩阵模拟，确定了DNA:RNA杂交双链体d(GTCACATG):r(caugugac)的溶液结构。该DNA:RNA杂交双链体在溶液中既不呈现A构象也不呈现B构象，而是一种中间的异源双链体结构。RNA链的糖具有正常的N型C3'-内构象，但DNA链的糖既没有N型也没有S型构象；相反，它们具有意想不到的中间O4'-内构象。碱基对的负x位移以及小的上升和正倾斜类似于A构象形态，但小沟宽度介于A构象和B构象双链体之间。DNA和RNA链在其螺旋参数上均表现出显著的序列依赖性变化。NOE和J耦合数据的联合分析表明，DNA糖不处于动态二态平衡。这种DNA:RNA杂交分子的详细三维结构导致了其与RNase H相互作用的一个提出的模型。与杂交双链体复合的酶的几个特定结构特征似乎解释了RNase H区分DNA:RNA杂交双链体和纯RNA:RNA双链体的机制。
