Huang Lin, Wang Jia, Lilley David M J
Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
Nucleic Acids Res. 2016 Jun 20;44(11):5390-8. doi: 10.1093/nar/gkw201. Epub 2016 Mar 25.
k-turns are commonly-occurring motifs that introduce sharp kinks into duplex RNA, thereby facilitating tertiary contacts. Both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called N3 and N1, that differ in the pattern of hydrogen bonding in the core. We show here that this is determined by the basepair adjacent to the critical G•A pairs. We determined crystal structures of a series of Kt-7 variants in which this 3b,3n position has been systematically varied, showing that this leads to a switch in the conformation. We have previously shown that the 3b,3n position also determines the folding characteristics of the k-turn, i.e. whether or not the k-turn can fold in the presence of metal ions alone. We have analyzed the distribution of 3b,3n sequences from four classes of k-turns from ribosomes, riboswitches and U4 snRNA, finding a strong conservation of properties for a given k-turn type. We thus demonstrate a strong association between biological function, 3b,3n sequence and k-turn folding and conformation. This has strong predictive power, and can be applied to the modeling of large RNA architectures.
k转角是常见的基序，可在双链RNA中引入急剧的弯折，从而促进三级相互作用。k转角的折叠和构象均由其局部序列决定。k转角分为两种构象类型，称为N3和N1，它们在核心区域的氢键模式上有所不同。我们在此表明，这是由与关键G•A碱基对相邻的碱基对决定的。我们确定了一系列Kt-7变体的晶体结构，其中3b,3n位置已被系统地改变，表明这会导致构象的转变。我们之前已经表明，3b,3n位置还决定了k转角的折叠特性，即k转角是否能仅在金属离子存在的情况下折叠。我们分析了来自核糖体、核糖开关和U4 snRNA的四类k转角的3b,3n序列分布，发现给定k转角类型的特性具有很强的保守性。因此，我们证明了生物学功能、3b,3n序列与k转角折叠和构象之间存在很强的关联。这具有很强的预测能力，可应用于大型RNA结构的建模。
