RNA helices are often punctuated with non-Watson–Crick features that may be targeted by chemical compounds, but progress toward identifying such compounds has been slow. We embedded a tandem UU:GA mismatch motif (5′-UG-3′:5′-AU-3′) within an RNA hairpin stem to identify compounds that bind the motif specifically. The three-dimensional structure of the RNA hairpin and its interaction with a small molecule identified through virtual screening are presented. The G-A mismatch forms a sheared pair upon which the U-U base pair stacks. The hydrogen bond configuration of the U-U pair involves O2 of the U adjacent to the G and O4 of the U adjacent to the A. The G-A and U-U pairs are flanked by A-U and G-C base pairs, respectively, and the stability of the mismatch is greater than when the motif is within the context of other flanking base pairs or when the 5′–3′ orientation of the G-A and U-U pairs is swapped. Residual dipolar coupling constants were used to generate an ensemble of structures against which a virtual screen of 64480 small molecules was performed. The tandem mismatch was found to be specific for one compound, 2-amino-1,3-benzothiazole-6-carboxamide, which binds with moderate affinity but extends the motif to include the flanking A-U and G-C base pairs. The finding that the affinity for the UU:GA mismatch is dependent on flanking sequence emphasizes the importance of the motif context and potentially increases the number of small noncanonical features within RNA that can be specifically targeted by small molecules.

中文翻译：

---

2-氨基-1,3-苯并噻唑-6-羧酰胺优先绑定串联错配基r（UY：GA）。

RNA螺旋通常带有非Watson-Crick特征的标记，这些特征可能是化学化合物靶向的，但鉴定此类化合物的进展缓慢。我们将串联的UU：GA不匹配基序（5'-UG-3'：5'-AU-3'）嵌入RNA发夹茎中，以鉴定与该基序特异性结合的化合物。介绍了RNA发夹的三维结构及其与通过虚拟筛选鉴定的小分子的相互作用。GA不匹配形成一个剪切对，UU碱基对堆叠在该剪切对上。UU对的氢键结构涉及与G相邻的U的O2和与A相邻的U的O4。GA和UU对分别侧接AU和GC碱基对，并且当基序在其他侧翼碱基对的上下文中或当GA和UU对的5'–3'方向互换时，错配的稳定性更大。残留的偶极偶合常数用于生成一组结构，针对该结构执行64480个小分子的虚拟筛选。发现串联错配对一种化合物2-氨基-1,3-苯并噻唑-6-羧酰胺具有特异性，该化合物以中等亲和力结合，但延伸了基序，包括侧翼的AU和GC碱基对。对UU：GA不匹配的亲和力取决于侧翼序列的发现强调了基序上下文的重要性，并可能增加了RNA内可被小分子特异性靶向的小非经典特征的数量。