Zhu L, Salazar M, Reid B R
Department of Chemistry, University of Washington, Seattle 98195.
Biochemistry. 1995 Feb 21;34(7):2372-80. doi: 10.1021/bi00007a033.
Hybrid duplexes and chimeric duplexes containing hybrid segments linked to pure DNA (or pure RNA) segments are involved in transcription and replication, as well as reverse transcription. A complete understanding of the mechanism of these processes requires detailed information on such duplexes and the junctions between duplexes of differing structure. Using two-dimensional NMR, restrained molecular dynamics and mechanics, and back-calculation refinement against the nuclear Overhauser effect spectra at various mixing times, we have determined the solution structure of the chimeric duplex [r(cgcg)d-(TATACGCG)]2 containing a pure DNA segment in the center of a hybrid duplex. The solution structure differs from the previously determined X-ray structure of the analogous duplex [r(gcg)d(TATACGC)]2, which was found to be A-form throughout [Wang, A.H.-J., et al. (1982) Nature 299, 601-604]. The basic features of the solution structure are (a) the RNA residues are all A-form with C3'-endo sugar conformations, (b) the central DNA segment is B-form, (c) the transition from A-form RNA sugar conformations to B-form DNA sugar conformations involves only the dT5 base step, and (d) although the sugar conformations of the DNA residues A6-G12 are closer to B-form, the basic helical properties of the peripheral RNA.DNA hybrid segments are closer to typical A-form than to B-form.
包含与纯DNA（或纯RNA）片段相连的杂合片段的杂交双链体和嵌合双链体参与转录、复制以及逆转录过程。要全面理解这些过程的机制，需要有关此类双链体以及不同结构双链体之间连接点的详细信息。利用二维核磁共振、受限分子动力学和力学，以及针对不同混合时间的核Overhauser效应谱进行反算精修，我们确定了嵌合双链体[r(cgcg)d-(TATACGCG)]2的溶液结构，该双链体在杂交双链体中心含有一个纯DNA片段。该溶液结构不同于之前测定的类似双链体[r(gcg)d(TATACGC)]2的X射线结构，后者在整个结构中均为A构型[王，A.H.-J.等人（1982年）《自然》299，601 - 604]。溶液结构的基本特征为：（a）RNA残基均为具有C3'-内向糖构象的A构型；（b）中心DNA片段为B构型；（c）从A构型RNA糖构象到B构型DNA糖构象的转变仅涉及dT5碱基步；（d）尽管DNA残基A6 - G12的糖构象更接近B构型，但外围RNA - DNA杂交片段的基本螺旋特性更接近典型的A构型而非B构型。
