Tang R S, Draper D E
Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218.
Biochemistry. 1994 Aug 23;33(33):10089-93. doi: 10.1021/bi00199a036.
We have used gel electrophoretic mobility measurements to investigate the conformation of the symmetric eubacterial loop E sequence of 5S rRNA (seven nucleotides in each strand). The loop strongly retarded the gel mobility of duplex RNAs containing it. In contrast, only asymmetric A5.An or U5.Un internal loops (n not equal to 5) strongly affected duplex RNA gel mobility. A phasing experiment, in which an A2 bulge and loop E were placed in the same duplex RNA and the number of base pairs between them varied, showed that loop E has a permanent bend and is torsionally stiff. A second phasing experiment substituting loop E for duplex sequences between two A2 bulges measured the helical twist associated with loop E; it is about 30 degrees (+/- 15 degrees) overwound compared to a duplex RNA of the same number of bases. Ribosomal protein L25 specifically recognizes loop E but had little or no effect on the twist of the loop. These results suggest that loop E adopts a specific, roughly helical structure.
我们利用凝胶电泳迁移率测量来研究5S rRNA对称真细菌环E序列（每条链七个核苷酸）的构象。该环极大地阻碍了含有它的双链RNA在凝胶中的迁移。相比之下，只有不对称的A5.An或U5.Un内环（n不等于5）会强烈影响双链RNA的凝胶迁移率。一项定相实验将一个A2凸起和环E置于同一双链RNA中，并改变它们之间的碱基对数，结果表明环E具有永久性弯曲且扭转刚性。第二项定相实验用环E替代两个A2凸起之间的双链序列，测量了与环E相关的螺旋扭转；与相同碱基数的双链RNA相比，它大约有30度（±15度）的过度缠绕。核糖体蛋白L25能特异性识别环E，但对环的扭转影响很小或没有影响。这些结果表明环E采用了一种特定的、大致呈螺旋状的结构。
