Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry. Issue 8 (20th January 2017)

• Record Type: Journal Article
• Authors: Shi, Xuesong; Walker, Peter; Harbury, Pehr B.; Herschlag, Daniel
• Is Part Of: Nucleic acids research. Volume 45:Issue 8(2017)
• Page Start: e64
• Page End: e64
• Publication Date: 2017-01-20
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkw1352
• Languages: English
• ISSNs: 0305-1048

Abstract

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.