Xiong Y, Sundaralingam M
The Ohio State University Biological Macromolecular Structure Center Departments of Chemistry, Biochemistry and Biophysics Program 012 Rightmire Hall 1060 Carmack Road Columbus Ohio 43210 USA.
Structure. 1998 Dec 15;6(12):1493-501. doi: 10.1016/s0969-2126(98)00148-8.
. DNA-RNA hybrids are substrates for RNase H. This enzyme catalyzes the hydrolysis of the RNA strand in the hybrid form. The polypurine tract (PPT) in human immunodeficiency virus 1 (HIV-1) is a short stretch of purines ( approximately 15 bases) located at the 3'-end of the U3 region of the RNA genome. The PPT has the unique ability to resist digestion by RNase H and serves as a primer for plus-strand DNA synthesis.
. The crystal structure of a DNA-RNA hybrid duplex containing a polypurine RNA strand, d(TTCTTBr5CTTC)-r(GAAGAAGAA), has been determined at 1.8 A resolution. The structure was solved by molecular replacement methods and refined to a final R factor of 20.1% (R free 23.7%). The hybrid duplex adopts a standard A-form conformation. All of the sugar rings and glycosidic torsion angles are found in the standard C3'-endo/anti conformation, as seen in A-RNA or A-DNA. The crystal packing is dominated by the DNA strand, where the terminal base pairs of the hybrid abut the neighboring A-DNA sugar-phosphate backbone on the minor groove side.
. The present DNA-RNA hybrid duplex containing a polypurine RNA strand exhibits standard A-form geometry. This observation might suggest that the RNA PPT resists the RNase H activity of HIV reverse transcriptase as a result of its A-form conformation. In addition, there appears to be a correlation between the percentage purine content of the RNA and the DNA backbone conformation.
DNA - RNA杂交体是核糖核酸酶H（RNase H）的作用底物。该酶催化杂交体形式中RNA链的水解。人类免疫缺陷病毒1型（HIV - 1）中的多聚嘌呤序列（PPT）是一段位于RNA基因组U3区域3'端的短嘌呤序列（约15个碱基）。PPT具有抵抗RNase H消化的独特能力，并作为正链DNA合成的引物。
已确定包含多聚嘌呤RNA链d(TTCTTBr5CTTC)-r(GAAGAAGAA)的DNA - RNA杂交双链体的晶体结构，分辨率为1.8 Å。该结构通过分子置换法解析，最终精修后的R因子为20.1%（自由R因子为23.7%）。杂交双链体采用标准的A构象。所有糖环和糖苷扭转角均处于标准的C3'-内/反式构象，如A - RNA或A - DNA中所见。晶体堆积以DNA链为主，杂交体的末端碱基对在小沟侧邻接相邻的A - DNA糖 - 磷酸骨架。
目前包含多聚嘌呤RNA链的DNA - RNA杂交双链体呈现标准的A形几何结构。这一观察结果可能表明，RNA PPT因其A形构象而抵抗HIV逆转录酶的RNase H活性。此外，RNA的嘌呤含量百分比与DNA骨架构象之间似乎存在相关性。
