2012 Fiscal Year Final Research Report

Investigation of intramolecular collision dynamics of RNA

Research Project

Project/Area Number	23750202
Research Category	Grant-in-Aid for Young Scientists (B)
Allocation Type	Multi-year Fund
Research Field	Chemistry related to living body
Research Institution	The Institute of Physical and Chemical Research
Principal Investigator	UZAWA Takanori 独立行政法人理化学研究所, 伊藤ナノ医工学研究室, 研究員 (60554376)
Project Period (FY)	2011 – 2012
Keywords	核酸 / 両末端の衝突速度 / ダイナミクス / ルテニウム錯体
Research Abstract	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.