title: Real-Time Monitoring of G-Quadruplex Formation during Transcription.
abstract: Cotranscriptional folding of an RNA transcript enables formation of metastable RNA structures. Thermodynamic and kinetic properties of RNA G-quadruplex formation have previously been investigated using purified guanine-rich oligonucleotides. Here, we describe a method for analysis of cotranscriptional dynamics of the G-quadruplex formation based on real-time monitoring of the fluorescence of G-quadruplex ligands. For RNA sequences with the potential to form mutually exclusive hairpin or G-quadruplex structures, the efficiency of G-quadruplex formation during transcription depended on position of the hairpin forming sequence. The real-time monitoring enabled evaluation of environmental effects on RNA dynamics, as we demonstrated facilitation of post-transcriptional G-quadruplex formation under molecular crowding conditions. The strategy demonstrated here provides folding insights into the G-quadruplex during transcription that should be involved in gene regulation.
authors.affiliation: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
authors.forename: Tamaki
authors.initials: T
authors.lastname: Endoh
authors.affiliation: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
authors.forename: Ambadas B
authors.initials: AB
authors.lastname: Rode
authors.affiliation: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
authors.forename: Shuntaro
authors.initials: S
authors.lastname: Takahashi
authors.affiliation: Graduate School of Science and Technology, Gunma University , 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
authors.forename: Yuka
authors.initials: Y
authors.lastname: Kataoka
authors.affiliation: Graduate School of Science and Technology, Gunma University , 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
authors.forename: Masayasu
authors.initials: M
authors.lastname: Kuwahara
authors.affiliation: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.|Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University , 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
mesh_terms: D001483:Base Sequence; D054856:G-Quadruplexes; D008024:Ligands; D009841:Oligonucleotides / Q000737:chemistry / Q000378:metabolism; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D013816:Thermodynamics; D014158:Transcription, Genetic
chemical_list: D008024:Ligands; D009841:Oligonucleotides; D012313:RNA