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A Method for Helical RNA Global Structure Determination in Solution Using Small-Angle X-Ray Scattering and NMR Measurements

  1. Author:
    Wang, J. B.
    Zuo, X. B.
    Yu, P.
    Xu, H.
    Starich, M. R.
    Tiede, D. M.
    Shapiro, B. A.
    Schwieters, C. D.
    Wang, Y. X.

  2. Author Address

    Wang, Jinbu, Zuo, Xiaobing, Yu, Ping, Xu, Huan, Wang, Yun-Xing] NCI, Prot Nucle Acid Interact Sect, Struct Biophys Lab, NIH, Frederick, MD 21702 USA. [Yu, Ping] SAIC Frederick Inc, NCI, NIH, Frederick, MD 21702 USA. [Starich, Mary R.] NCI, Off Chief, Struct Biophys Lab, NIH, Frederick, MD 21702 USA. [Tiede, David M.] Argonne Natl Lab, Chem Sci & Engn Div, Argonne, IL 60439 USA. [Shapiro, Bruce A.] NCI, Ctr Canc Res Nanobiol Program, NIH, Frederick, MD 21702 USA. [Schwieters, Charles D.] NIH, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA.
    1. Year: 2009
  2. Journal: Journal of Molecular Biology
    1. 393
    2. 3
    3. Pages: 717-734
  4. Type of Article: Article
  1. Abstract:

    We report a "top-down" method that uses mainly duplexes' global orientations and overall molecular dimension and shape restraints, which were extracted from experimental NMR and small-angle X-ray scattering data, respectively, to determine global architectures of RNA molecules consisting of mostly A-form-like duplexes. The method is implemented in the G2G (from global measurement to global structure) toolkit of programs. We demonstrate the efficiency and accuracy of the method by determining the global structure of a 71-nt RNA using experimental data. The backbone root-mean-square deviation of the ensemble of the calculated global structures relative to the X-ray crystal structure is 3.0 +/- 0.3 angstrom using the experimental data and is only 2.5 +/- 0.2 angstrom for the three duplexes that were orientation restrained during the calculation. The global structure simplifies interpretation of multidimensional nuclear Overhauser spectra for high-resolution structure determination. The potential general application of the method for RNA structure determination is discussed. Published by Elsevier Ltd.

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  2. DOI: 10.1016/j.jmb.2009.08.001
  3. PMID: 19666030

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