Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
Nucleic Acids Res. 2009 Nov;37(21):7281-9. doi: 10.1093/nar/gkp791.
Kink turns (k-turns) are important structural motifs that create a sharp axial bend in RNA. Most conform to a consensus in which a three-nucleotide bulge is followed by consecutive GA and AG base pairs, and when these GA pairs are modified in vitro this generally leads to a failure to adopt the k-turn conformation. Kt-23 in the 30S ribosomal subunit of Thermus thermophilus is a rare exception in which the bulge-distal AG pair is replaced by a non-Watson-Crick AU pair. In the context of the ribosome, Kt-23 adopts a completely conventional k-turn geometry. We show here that this sequence is induced to fold into a k-turn structure in an isolated RNA duplex by Mg(2+) or Na(+) ions. Therefore, the Kt-23 is intrinsically stable despite lacking the key AG pair; its formation requires neither tertiary interactions nor protein binding. Moreover, the Kt-23 k-turn is stabilized by the same critical hydrogen-bonding interactions within the core of the structure that are found in more conventional sequences such as the near-consensus Kt-7. T. thermophilus Kt-23 has two further non-Watson-Crick base pairs within the non-canonical helix, three and four nucleotides from the bulge, and we find that the nature of these pairs influences the ability of the RNA to adopt k-turn conformation, although the base pair adjacent to the A*U pair is more important than the other.
发夹环（k-turns）是 RNA 中形成尖锐轴向弯曲的重要结构基序。大多数发夹环都符合一个共识，其中三核苷酸凸起后面是连续的 GA 和 AG 碱基对，并且当这些 GA 对在体外进行修饰时，通常会导致无法采用 k-turn 构象。嗜热菌 30S 核糖体亚基中的 Kt-23 是一个罕见的例外，其中凸起远端的 AG 对被非 Watson-Crick AU 对取代。在核糖体的背景下，Kt-23 采用完全常规的 k-turn 几何形状。我们在这里表明，在孤立的 RNA 双链体中，Mg(2+)或 Na(+)离子诱导该序列折叠成 k-turn 结构。因此，尽管缺乏关键的 AG 对，Kt-23 是固有稳定的；其形成既不需要三级相互作用也不需要蛋白质结合。此外，Kt-23 k-turn 由结构核心内的相同关键氢键相互作用稳定，这些相互作用在更常规的序列中也存在，例如近共识的 Kt-7。T. thermophilus Kt-23 在非典型螺旋内还有另外两个非 Watson-Crick 碱基对，距离凸起三个和四个核苷酸，我们发现这些碱基对的性质会影响 RNA 采用 k-turn 构象的能力，尽管与 A*U 对相邻的碱基对比其他碱基对更为重要。
