Investigation of intramolecular collision dynamics of RNA

蛋白质和寡核苷酸的三维结构的形成需要分子内相互作用的逐步形成，这表明分子内碰撞是三维结构形成的最基本过程。尽管非结构多肽的分子内碰撞动力学已经得到了广泛的研究，但寡核苷酸的分子内碰撞动力学研究还很有限。因此，在这项研究中，我的目标是研究DNA和RNA的寡核苷酸的端到端碰撞率的碱基组成、链长和温度的依赖关系。我使用在寡核苷酸末端修饰的发光团的寿命来测量分子内碰撞动力学，该发光团的另一端被猝灭剂修饰。对于长度超过20个碱基的DNA，在较低的温度下，多聚腺嘌呤的构象变化有助于端到端的碰撞动力学。然而，在高温下，这种贡献消失了，多腺嘌呤的动力学与多胸腺嘧啶的动力学相对应。对RNA的类似实验没有显示出存在猝灭剂和不存在猝灭剂之间的发光体寿命的明显差异。

Formation of three dimensional structures of a protein and an oligonucleotide require stepwise formation of intramolecular interactions, indicating that intramolecular collision is the most essential process of 3D structure formation. Although the intraolecular collision dynamics of unstructured polypeptides have seen extensively studied, those of oligonucleotides are limited. Thus motivated, in this study I aimed to investigate the base-composition, chain-length and temperature dependences of the end-to-end collision rates for both oligonucleotides of DNA and RNA. I measured the intramolecular collision dynamics using lifetime of a luminophore modified at the end of a oligonucleotide whose the other terminal was modified with a quencher. For a DNA over 20 bases in length, conformational change of polyadenine contributes on the end-to-end collision dynamics at lower temperature. At high temperature, however, this contribution disappears and the dynamics of polyadenine corresponds to the dynamics of polythymine. A similar experiment on RNA did not exhibit clear difference of the luminophore lifetimes between with presence of the quencher and absence of the quencher.