Crystal structure of a DNA.RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC).
Crystal structure of a DNA.RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC).
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DOI：
10.1093/nar/28.10.2171
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发表时间：
2000-05
影响因子：
14.9
通讯作者：
Y. Xiong;M. Sundaralingam
中科院分区：
文献类型：
--
作者：
Y. Xiong;M. Sundaralingam
DNA、RNA杂交双链体是RNase H和逆转录酶的底物。具有多嘌呤RNA链和互补DNA链的杂合双链体d（5 '-CTCTTCTTC-3'）.r（5 '-gaagaagag-3'）（其中的小写字母表示DNA，小写字母表示RNA）的晶体结构已在1.8 A分辨率下测定。首先通过XPLOR在1.9 A下精制结构，随后通过CNS在1.8 A下精制结构。发现该杂合物具有标准的A型构象，其中所有糖都在C3 '-内切起皱中。DNA链的5 '末端碱基dC在本结构的电子密度图中清晰可见，与之前报道的结构d（TTCTTBr（5）CTTC）.r（gaagaagaa）形成鲜明对比，其中5'末端碱基dT不可见，导致末端rA未配对。因此，在两种混合晶体结构中，末端碱基对C.g与T. a的比较提供了关于这些碱基对在氢键（三对二）和碱基堆积相互作用中的稳定性的信息。末端碱基对的差异在两种结构中产生不同的扭结。在本结构中观察到小沟加宽，位于双链体下半部分的独特扭结处，与小沟的小幅加宽和T. a结构上半部分的非常轻微的弯曲形成对比。
DNA.RNA hybrid duplexes are substrates of RNase H and reverse transcriptase. The crystal structure of a hybrid duplex, d(5'-CTCTTCTTC-3').r(5'-gaagaagag-3') (the uppercase letters indicate DNA and lowercase letters RNA), with a polypurine RNA strand and a complementary DNA strand has been determined at 1.8 A resolution. The structure was refined first at 1.9 A by XPLOR and subsequently by CNS at 1.8 A. The hybrid is found in a standard A-form conformation with all the sugars in the C3'-endo puckering. The 5'-terminal base dC of the DNA strand was clearly visible in the electron density map of the present structure, in contrast to the previously reported structure d(TTCTTBr(5)CTTC).r(gaagaagaa) where the 5'-terminal base dT was not visible, leaving the terminal rA unpaired. Thus, the comparison of the terminal base pairs, C.g versus T.a, in the two hybrid crystal structures provides information on the stability of these base pairs in hydrogen bonding (three versus two) and base stacking interactions. The differences in the terminal base pairs produce different kinks in the two structures. Minor groove widening is observed in the present structure at a distinctive kink in the lower half of the duplex, in contrast to the small widening of the minor groove and a very slight bend in the upper half of the T.a structure.