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Evaluation of Dynamic Features of Escherichia coli 16S Ribosomal RNA in Homogeneous Physiological Solution

Takashi Sakamoto ^*, Atsushi Mahara , Koichi Yamagata , Reiko Iwase , Tetsuji Yamaoka  and Akira Murakami ^*

^* Department of Polymer Science and Engineering, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Japan; Department of Biomedical Engineering, Advanced Medical Engineering Center, National Cardiovascular Center Research Institute, Suita, Osaka, Japan; BMI Laboratory, Central Research Laboratories, Sysmex Corporation, Kobe, Hyogo, Japan; and Department of Bioscience, Teikyo University of Science and Technology, Uenohara, Yamanashi, Japan

Correspondence: Address reprint requests to Akira Murakami, E-mail: akiram{at}kit.ac.jp.

There is no methodology for the estimation of the dynamic features of large-molecular-weight RNAs in homogeneous physiological media. In this report, a luminescence anisotropy-based method using a long-lifetime luminescent oligonucleotide probe for the estimation of the dynamic features of large-molecular-weight RNA is described. As a luminescent probe, Ru(II) complex-labeled oligonucleotides, which have a complementary sequence to the single-stranded regions of Escherichia coli 16S rRNA, were synthesized. After the hybridization of the probe to single-stranded regions of 16S rRNA, the segmental motions of the regions were evaluated by time-resolved luminescence anisotropy analysis. In 16S rRNA, the L2 site (323–332 nt) was found to be the most flexible among the seven sites chosen. From a comparison between the hybridization kinetics of oligonucleotides to these single-stranded regions and the rotational correlation times, it was suggested that the flexibility of the single-stranded region was closely correlated with the hybridization kinetics. Furthermore, results of the luminescence lifetime measurement and luminescence quenching experiments suggested that the highly flexible region was located on the surface of the 16S rRNA and that the less flexible region was located in the depths of 16S rRNA.