title: Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry.
abstract: The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures. We show that the XSI-based model of the TAR RNA ensemble closely resembles an independent model derived from NMR-RDC data. Further, we show how the TAR RNA ensemble changes shape at different salt concentrations. Finally, we demonstrate that a single hybrid model of the TAR RNA ensemble simultaneously fits both the XSI and NMR-RDC data set and show that XSI can be combined with NMR-RDC to further improve the quality of the determined ensemble. The results suggest that XSI-RNA will be a powerful approach for characterizing the solution conformational ensembles of RNAs and RNA-protein complexes under diverse solution conditions.
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
authors.forename: Xuesong
authors.initials: X
authors.lastname: Shi
authors.affiliation: Protein and Nucleic Acids Facility, Stanford University, Stanford, CA 94305, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Walker
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.|Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
authors.forename: Pehr B
authors.initials: PB
authors.lastname: Harbury
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.|Department of Chemistry, Stanford University, Stanford, CA 94305, USA.|Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Herschlag
mesh_terms: D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000737:chemistry*; D007368:Interferometry / Q000379:methods*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D053758:Nanoparticles / Q000737:chemistry; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D012542:Scattering, Radiation; D012834:Silver / Q000737:chemistry*; D013194:Staining and Labeling / Q000379:methods; D014965:X-Rays
chemical_list: D012367:RNA, Viral; D012834:Silver