Colvin R A, White S W, Garcia-Blanco M A, Hoffman D W
Department of Microbiology, Duke University Medical Center, Durham, North Carolina 27710.
Biochemistry. 1993 Feb 2;32(4):1105-12. doi: 10.1021/bi00055a016.
A 19-nucleotide RNA containing the CUGGGA loop sequence corresponding to nucleotides 30-35 of the HIV-1 trans-activation response element (TAR) was synthesized in vitro and analyzed by biochemical methods and one- and two-dimensional NMR spectroscopy. Diagnostic RNase cleavage patterns were similar for the loops in the full-length HIV-1 TAR and the 19-nucleotide RNA, indicating that they are similar in structure. NMR data showed that the loop is stabilized by base-stacking interactions. The first loop nucleotide is stacked upon the A-helical stem, and the loop uridine is stacked upon this cytosine. On the opposite side of the loop, the third loop guanosine is stacked upon the adenosine, which is stacked upon the stem. No specific Watson-Crick or non-Watson-Crick base pairing across the loop was identified. Unusually short interribose distances indicate a significant distortion of the sugar-phosphate backbone centered at the adenosine. Relatively short NMR relaxation times for protons of the adenosine and its adjacent guanosine, as well as rapidly exchanging imino protons, provide evidence for dynamic processes occurring in the loop.
体外合成了一种包含与HIV-1反式激活应答元件（TAR）核苷酸30 - 35相对应的CUGGGA环序列的19核苷酸RNA，并通过生化方法以及一维和二维核磁共振光谱进行分析。全长HIV-1 TAR中的环与19核苷酸RNA中的环的诊断性核糖核酸酶切割模式相似，表明它们在结构上相似。核磁共振数据表明，该环通过碱基堆积相互作用得以稳定。环的第一个核苷酸堆积在A螺旋茎上，环尿苷堆积在这个胞嘧啶上。在环的另一侧，环的第三个鸟苷堆积在腺苷上，而腺苷又堆积在茎上。未发现环上存在特定的沃森-克里克或非沃森-克里克碱基配对。异常短的核糖间距离表明以腺苷为中心的糖磷酸骨架发生了显著扭曲。腺苷及其相邻鸟苷质子的相对较短的核磁共振弛豫时间，以及快速交换的亚氨基质子，为环中发生的动态过程提供了证据。
