title: Intrinsic flexibility of snRNA hairpin loops facilitates protein binding.
abstract: Stem-loop II of U1 snRNA and Stem-loop IV of U2 snRNA typically have 10 or 11 nucleotides in their loops. The fluorescent nucleobase 2-aminopurine was used as a substitute for the adenines in each loop to probe the local and global structures and dynamics of these unusually long loops. Using steady-state and time-resolved fluorescence, we find that, while the bases in the loops are stacked, they are able to undergo significant local motion on the picosecond/nanosecond timescale. In addition, the loops have a global conformational change at low temperatures that occurs on the microsecond timescale, as determined using laser T-jump experiments. Nucleobase and loop motions are present at temperatures far below the melting temperature of the hairpin stem, which may facilitate the conformational change required for specific protein binding to these RNA loops.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri 63110, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Rau
authors.forename: W Tom
authors.initials: WT
authors.lastname: Stump
authors.forename: Kathleen B
authors.initials: KB
authors.lastname: Hall
mesh_terms: D015075:2-Aminopurine / Q000737:chemistry; D000818:Animals; D001483:Base Sequence; D004330:Drosophila; D029721:Drosophila Proteins / Q000737:chemistry; D005454:Fluorescence Polarization; D005456:Fluorescent Dyes / Q000737:chemistry; D006801:Humans; D055029:Inverted Repeat Sequences; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012342:RNA, Small Nuclear / Q000737:chemistry*; D011817:Rabbits; D012261:Ribonucleoproteins / Q000737:chemistry; D013050:Spectrometry, Fluorescence; D044366:Transition Temperature
chemical_list: D029721:Drosophila Proteins; D005456:Fluorescent Dyes; D012342:RNA, Small Nuclear; D012261:Ribonucleoproteins; C405483:U1 small nuclear RNA; C405484:U2 small nuclear RNA; D015075:2-Aminopurine