Konno Keisuke, Iizuka Mana, Fujita Syusuke, Nishikawa Satoshi, Hasegawa Tsunemi, Fukuda Kotaro
Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, Japan.
Nucleosides Nucleotides Nucleic Acids. 2011 Mar;30(3):185-202. doi: 10.1080/15257770.2011.562475.
The higher order structure of HCV (-)IRES containing five stem-loop structures (domain I) is essential for HCV replication because the viral RNA-dependent RNA polymerase, NS5B, recognizes it as the initiation site for plus-strand synthesis. To inhibit a de novo synthesis of plus-strand RNA molecules, in vitro selection against (-)IRES domain I was performed. One of the obtained aptamers, AP30, contained two consensus sequences within a random sequence region. Two consensus sequences form two apical loops and mutational analysis showed that both sequences were essential for binding to the target and for inhibiting NS5B-mediated RNA synthesis in vitro.
