Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
Nanoscale. 2016 Aug 18;8(33):15189-95. doi: 10.1039/c6nr05186c.
k-Turns are widespread RNA architectural elements that mediate tertiary interactions. We describe a double-kink-turn motif comprising two inverted k-turns that forms a tight horse-shoe structure that can assemble into a variety of shapes by coaxial association of helical ends. Using X-ray crystallography we show that these assemble with two (dumbell), three (triangle) and four units (square), with or without bound protein, within the crystal lattice. In addition, exchange of a single basepair can almost double the pore radius or shape of a molecular assembly. On the basis of this analysis we synthesized a 114 nt self-complementary RNA containing six k-turns. The crystal structure of this species shows that it forms a quasi-cyclic triangular object. These are randomly disposed about the three-fold axis in the crystal lattice, generating a circular RNA of quasi D3 symmetry with a shape reminiscent of that of a cyclohexane molecule in its chair conformation. This work demonstrates that the k-turn is a powerful building block in the construction of nano-scale molecular objects, and illustrates why k-turns are widely used in natural RNA molecules to organize long-range architecture and mediate tertiary contacts.
k-turns 是广泛存在的 RNA 结构元件，介导三级相互作用。我们描述了一种双扭结结构，由两个反向的 k-turn 组成，形成一个紧密的马蹄铁结构，可以通过螺旋末端的同轴缔合形成各种形状。使用 X 射线晶体学，我们表明这些结构可以在晶格中与两个（哑铃）、三个（三角形）和四个单元（正方形）组装在一起，有或没有结合的蛋白质。此外，单个碱基对的交换几乎可以使分子组装的孔径或形状增加一倍。在此基础上，我们合成了一个包含六个 k-turn 的 114 个核苷酸的自我互补 RNA。该物种的晶体结构表明，它形成了一个准循环三角形物体。这些在晶格中围绕三重轴随机分布，在晶体中生成一个具有准 D3 对称性的圆形 RNA，其形状类似于环己烷分子在椅式构象中的形状。这项工作表明 k-turn 是构建纳米尺度分子物体的有力构件，并说明了为什么 k-turn 在天然 RNA 分子中被广泛用于组织远程结构并介导三级接触。
