Conn G L, Brown T, Leonard G A
Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK and Joint ESRF/EMBLStructural Biology Group, European Synchrotron Radiation Facility, BP 200, F-38034 Grenoble Cedex, France.
Nucleic Acids Res. 1999 Jan 15;27(2):555-61. doi: 10.1093/nar/27.2.555.
The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC). d(GCTTCTCTTC) has been solved and refined at 2.5 A resolution. The refinement procedure converged at R = 0.181 for all reflections in the range 20.0-2.5 A. In the crystal, the RNA/DNA hybrid duplex has an A' conformation with all but one of the nucleotide sugar moieties adopting a C3'- endo (N) conformation. Both strands in the double helix adopt a global conformation close to the A-form and the width of the minor groove is typical of that found in the crystal structures of other A-form duplexes. However, differences are observed between the RNA and DNA strands that make up the hybrid at the local level. In the central portion of the duplex, the RNA strand has backbone alpha, beta and gamma torsion angles that alternate between the normal gauche -/ trans / gauche + conformation and an unusual trans / trans / trans conformation. Coupled with this so-called 'alpha/gamma flipping' of the backbone torsion angles, the distance between adjacent phosphorous atoms on the RNA strand systematically varies. Neither of these phenomena are observed on the DNA strand. The structure of the RNA/DNA hybrid presented here differs significantly from that found in solution for this and other sequences. Possible reasons for these differences and their implications for the current model of RNase H activity are discussed.
RNA/DNA杂交体r(GAAGAGAAGC).d(GCTTCTCTTC)的晶体结构已在2.5埃分辨率下解析并精修。精修过程对于20.0 - 2.5埃范围内的所有反射在R = 0.181处收敛。在晶体中，RNA/DNA杂交双链体具有A'构象，除一个核苷酸糖部分外，所有核苷酸糖部分均采用C3'-内型（N）构象。双螺旋中的两条链均采用接近A-型的整体构象，小沟宽度是其他A-型双链体晶体结构中典型的宽度。然而，在局部水平上，构成杂交体的RNA链和DNA链之间存在差异。在双链体的中央部分，RNA链的骨架α、β和γ扭转角在正常的左/反式/右+构象和不寻常的反式/反式/反式构象之间交替。伴随着这种所谓的骨架扭转角“α/γ翻转”，RNA链上相邻磷原子之间的距离系统性地变化。在DNA链上未观察到这些现象中的任何一种。此处呈现的RNA/DNA杂交体结构与该序列及其他序列在溶液中发现的结构有显著差异。讨论了这些差异的可能原因及其对当前核糖核酸酶H活性模型的影响。
