title: Guanine is indispensable for immunoglobulin switch region RNA-DNA hybrid formation.
abstract: It is suggested that the formation of the switch (S) region RNA-DNA hybrid and the subsequent generation of higher-order chromatin structures including R-loop initiate a class switch recombination of the immunoglobulin gene. The primary factor of this recombination is the S-region derived noncoding RNA. However, the biochemical character of this guanine-rich (G-rich) transcript is poorly understood. The present study was performed to analyze the structure of this G-rich RNA using atomic force microscope (AFM). The in vitro transcribed S-region RNA was spread on a mica plate, air-dried and observed by non-contact mode AFM in air. The G-rich transcripts tend to aggregate on the template DNA and to generate a higher-order RNA-DNA complex. However, the transcripts that incorporated guanine analogues as substitutes for guanine neither aggregated nor generated higher-order structures. Incorporation of guanine analogues in transcribed RNA partially disrupts hydrogen bonds related to guanine, such as Watson-Crick GC-base pair and Hoogsteen bond GG-base pair. Thus, aggregation of S-region RNA and generation of the higher-order RNA-DNA complex are attributed to hydrogen bonds of guanine.
authors.affiliation: Research Institute for Biological Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan. mizuta@rs.noda.tus.ac.jp
authors.forename: Ryushin
authors.initials: R
authors.lastname: Mizuta
authors.forename: Midori
authors.initials: M
authors.lastname: Mizuta
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kitamura
mesh_terms: D004247:DNA / Q000737:chemistry / Q000378:metabolism* / Q000648:ultrastructure; D006147:Guanine / Q000737:chemistry*; D017578:Immunoglobulin Class Switching; D007134:Immunoglobulin Switch Region / Q000235:genetics*; D018625:Microscopy, Atomic Force / Q000379:methods*; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism* / Q000648:ultrastructure; D011995:Recombination, Genetic
chemical_list: D006147:Guanine; D012313:RNA; D004247:DNA