Resolving the motional modes that code for RNA adaptation.
Using a domain elongation strategy, we decoupled internal motions in RNA from overall rotational diffusion. This allowed us to site-specifically resolve a manifold of motional modes in two regulatory RNAs from HIV-1 with the use of nuclear magnetic resonance spin relaxation methods. Base and sugar librations vary on a picosecond time scale and occur within helical domains that move collectively at diffusion-limited nanosecond time scales. Pivot points are short, functionally important, and highly mobile internal loops. These spontaneous changes in RNA conformation correlate quantitatively with those that follow adaptive recognition of diverse targets. Thus, ligands may stabilize existing RNA conformations rather than inducing new ones.
Zhang
Qi
Q
Department of Chemistry and Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA.
Sun
Xiaoyan
X
Watt
Eric D
ED
Al-Hashimi
Hashim M
HM
D001120:Arginine / Q000031:analogs & derivatives / Q000378:metabolism; D020029:Base Pairing; D006147:Guanine / Q000737:chemistry; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000235:genetics*; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012330:RNA, Double-Stranded / Q000737:chemistry / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D012399:Rotation; D014529:Uridine / Q000737:chemistry
D012330:RNA, Double-Stranded; D012367:RNA, Viral; C069339:argininamide; D006147:Guanine; D001120:Arginine; D014529:Uridine