Conn G L, Gutell R R, Draper D E
Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA.
Biochemistry. 1998 Aug 25;37(34):11980-8. doi: 10.1021/bi980825+.
Comparative sequence analysis reveals a coordinated set of nucleotide exchanges between the base pair 1092/1099 and the unpaired position 1072 [(1092/1099)1072] in the L11 binding domain of 23S ribosomal RNA. This set of exchanges has occurred at least 4 times during evolution, suggesting that these positions form a base triple. The analysis further suggests an important role for positions (1065/1073), adjacent to 1072. The covariation at positions (1092/1099)1072 is studied here by analysis of RNA variants using UV melting and binding of ribosomal protein L11 and thiostrepton to assay for tertiary folding of this domain. The tertiary structure of the RNA is eliminated by alteration of the unpaired nucleotide (C1072 to U mutation), and binding of L11 and thiostrepton are reduced 10-fold compared to the wild type. In contrast, substitution of the base pair (CG1092/1099 to UA mutation) allows formation of the tertiary structure but dramatically alters the pH dependence of tertiary folding. The fully compensated set of mutations, (CG)C to (UA)U, restores the tertiary structure of the RNA to a state almost identical to the wild type. The nature of this base triple and its implications for the folding of the RNA and ligand interactions are discussed.
比较序列分析揭示了23S核糖体RNA的L11结合结构域中碱基对1092/1099与未配对位置1072[（1092/1099）1072]之间存在一组协同的核苷酸交换。在进化过程中，这组交换至少发生了4次，表明这些位置形成了一个碱基三联体。分析还表明，与1072相邻的位置（1065/1073）具有重要作用。本文通过对RNA变体进行紫外熔解分析，以及利用核糖体蛋白L11和硫链丝菌素的结合来检测该结构域的三级折叠，研究了（1092/1099）1072位置的共变情况。RNA的未配对核苷酸发生改变（C1072突变为U）会破坏RNA的三级结构，与野生型相比，L11和硫链丝菌素的结合减少了10倍。相反，碱基对（CG1092/1099突变为UA）的替换允许形成三级结构，但显著改变了三级折叠的pH依赖性。完全补偿的突变组（CG）C变为（UA）U，可将RNA的三级结构恢复到几乎与野生型相同的状态。本文讨论了这种碱基三联体的性质及其对RNA折叠和配体相互作用的影响。
