STRUCTURE OF A DNA-RNA HYBRID DUPLEX - WHY RNASE-H DOES NOT CLEAVE PURE RNA

被引:233
作者
FEDOROFF, OY
SALAZAR, M
REID, BR
机构
[1] UNIV WASHINGTON,DEPT CHEM,SEATTLE,WA 98195
[2] UNIV WASHINGTON,DEPT BIOCHEM,SEATTLE,WA 98195
[3] RUSSIAN ACAD SCI,INST MATH PROBLEMS BIOL,PUSHCHINO 142292,RUSSIA
关键词
NMR; DNA-RNA HYBRID; SOLUTION STRUCTURE; RNASE-H;
D O I
10.1006/jmbi.1993.1528
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 cursive greek chi-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.
引用
收藏
页码:509 / 523
页数:15
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