title: Groove modification of siRNA duplexes to elucidate siRNA-protein interactions using 7-bromo-7-deazaadenosine and 3-bromo-3-deazaadenosine as chemical probes.
abstract: Elucidation of dynamic interactions between RNA and proteins is essential for understanding the biological processes regulated by RNA, such as RNA interference (RNAi). In this study, the logical chemical probes, comprising 7-bromo-7-deazaadenosine (Br7C7A) and 3-bromo-3-deazaadenosine (Br3C3A), to investigate small interfering RNA (siRNA)-RNAi related protein interactions, were developed. The bromo substituents of Br7C7A and Br3C3A are expected to be located in the major and the minor grooves, respectively, and to act as a steric hindrance in each groove when these chemical probes are incorporated into siRNAs. A comprehensive investigation using siRNAs containing these chemical probes revealed that (i) Br3C3A(s) at the 5'-end of the passenger strand enhanced their RNAi activity, and (ii) the direction of RISC assembly is determined by the interaction between Argonaute2, which is the main component of RISC, and siRNA in the minor groove near the 5'-end of the passenger strand. Utilization of these chemical probes enables the investigation of the dynamic interactions between RNA and proteins.
authors.affiliation: Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan. minakawa@tokushima-u.ac.jp.
authors.forename: Noriko
authors.initials: N
authors.lastname: Saito-Tarashima
authors.affiliation: Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan. minakawa@tokushima-u.ac.jp.
authors.forename: Hirotaka
authors.initials: H
authors.lastname: Kira
authors.affiliation: Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan. minakawa@tokushima-u.ac.jp.
authors.forename: Tomoya
authors.initials: T
authors.lastname: Wada
authors.affiliation: Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan. minakawa@tokushima-u.ac.jp.
authors.forename: Kazuya
authors.initials: K
authors.lastname: Miki
authors.affiliation: Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
authors.forename: Shiho
authors.initials: S
authors.lastname: Ide
authors.affiliation: Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan. minakawa@tokushima-u.ac.jp.
authors.forename: Naoshi
authors.initials: N
authors.lastname: Yamazaki
authors.affiliation: Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Matsuda
authors.affiliation: Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan. minakawa@tokushima-u.ac.jp.
authors.forename: Noriaki
authors.initials: N
authors.lastname: Minakawa
mesh_terms: D000241:Adenosine / Q000737:chemistry*; D001483:Base Sequence; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011506:Proteins / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D014372:Tubercidin / Q000737:chemistry*
chemical_list: D011506:Proteins; D034741:RNA, Small Interfering; D000241:Adenosine; D014372:Tubercidin