Flaviviruses such as Zika (ZIKV) and dengue virus (DENV) are positive-sense RNA viruses belonging to Flaviviridae. The flavivirus genome contains a 5’ end stem-loop promoter sequence known as stem-loop A (SLA) that is recognized by the flavivirus polymerase NS5 during viral RNA synthesis and 5’ guanosine cap methylation. The crystal structures of ZIKV and DENV SLAs show a well-defined fold, consisting of a bottom stem, side loop, and top stem-loop, providing unique interaction sites for small-molecule inhibitors to disrupt the promoter function. To facilitate identification of small molecule binding sites in flavivirus SLA, we determined high-resolution structures of bottom and top stems of ZIKV SLA, which contain a single U- or G-bulge, respectively. Both bulge nucleotides exhibit multiple orientations, from folded back on the adjacent nucleotide to flipped out of the helix, and are stabilized by stacking or base triple interactions. These structures suggest that even a single unpaired nucleotide can provide flexibility to RNA structures and its conformation is mainly determined by the stabilizing chemical environment. To facilitate discovery of small molecule inhibitors that interfere with the functions of ZIKV SLA, we screened and identified compounds that bind to the bottom and top stems of ZIKV SLA.

中文翻译：

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寨卡病毒茎环 A 中的高分辨率 RNA 三级结构用于抑制性小分子的开发

寨卡病毒（ZIKV）和登革热病毒（DENV）等黄病毒是属于黄病毒科的正链RNA病毒。黄病毒基因组包含称为茎环 A (SLA) 的 5' 末端茎环启动子序列，在病毒 RNA 合成和 5' 鸟苷帽甲基化过程中被黄病毒聚合酶 NS5 识别。ZIKV 和 DENV SLA 的晶体结构显示出明确的折叠，由底部茎、侧环和顶部茎环组成，为小分子抑制剂破坏启动子功能提供了独特的相互作用位点。为了便于识别黄病毒 SLA 中的小分子结合位点，我们确定了 ZIKV SLA 底部和顶部茎的高分辨率结构，它们分别包含单个 U 或 G 凸起。两种凸出核苷酸都表现出多种方向，从在相邻核苷酸上折回到翻转出螺旋，并且通过堆叠或碱基三重相互作用来稳定。这些结构表明，即使是单个未配对的核苷酸也可以为RNA结构提供灵活性，其构象主要由稳定的化学环境决定。为了促进发现干扰 ZIKV SLA 功能的小分子抑制剂，我们筛选并鉴定了与 ZIKV SLA 底部和顶部茎结合的化合物。