A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements.

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 A using the experimental data and is only 2.5+/-0.2 A 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.

[1]  Wolfram Saenger,et al.  Principles of Nucleic Acid Structure , 1983 .

[2]  K. Wüthrich.  NMR of proteins and nucleic acids , 1988 .

[3]  E. Westhof,et al.  Geometric nomenclature and classification of RNA base pairs. , 2001, RNA.

[4]  O. Glatter,et al.  19 – Small-Angle X-ray Scattering , 1973 .

[5]  J. Prestegard,et al.  Domain orientation and dynamics in multidomain proteins from residual dipolar couplings. , 1999, Biochemistry.

[6]  K. Weeks,et al.  RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). , 2005, Journal of the American Chemical Society.

[7]  Qi Zhang,et al.  Resolving the Motional Modes That Code for RNA Adaptation , 2006, Science.

[8]  A. Serganov,et al.  Ribozymes, riboswitches and beyond: regulation of gene expression without proteins , 2007, Nature Reviews Genetics.

[9]  Joseph D Puglisi,et al.  Structure of HCV IRES domain II determined by NMR , 2003, Nature Structural Biology.

[10]  Dmitri I. Svergun,et al.  Determination of the regularization parameter in indirect-transform methods using perceptual criteria , 1992 .

[11]  C. Schwieters,et al.  Global molecular structure and interfaces: refining an RNA:RNA complex structure using solution X-ray scattering data. , 2008, Journal of the American Chemical Society.

[12]  J. Maizel,et al.  RNA2D3D: A program for Generating, Viewing, and Comparing 3-Dimensional Models of RNA , 2008, Journal of biomolecular structure & dynamics.

[13]  西村 善文.  W. Saenger: Principles of Nucleic Acid Structure, Springer-Verlag, New York and Berlin, 1984, xx+556ページ, 24.5×16.5cm, 14,160円 (Springer Advanced Texts in Chemistry). , 1985 .

[14]  Michael Zuker,et al.  RNA Secondary Structure Prediction , 2007, Current protocols in nucleic acid chemistry.

[15]  Charles K. Fisher,et al.  Visualizing spatially correlated dynamics that directs RNA conformational transitions , 2007, Nature.

[16]  S. Grzesiek,et al.  Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy. , 1999, Nucleic acids research.

[17]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[18]  J H Prestegard,et al.  Order matrix analysis of residual dipolar couplings using singular value decomposition. , 1999, Journal of magnetic resonance.

[19]  A M Gronenborn,et al.  Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude. , 1998, Journal of magnetic resonance.

[20]  Dmitri I. Svergun,et al.  Automated matching of high- and low-resolution structural models , 2001 .

[21]  M. Summers,et al.  NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus. , 2004, Journal of molecular biology.

[22]  Charles D Schwieters,et al.  The Xplor-NIH NMR molecular structure determination package. , 2003, Journal of magnetic resonance.

[23]  Kenneth M Merz,et al.  X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[24]  A. Bax,et al.  Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. , 1998, Journal of magnetic resonance.

[25]  F. Major,et al.  The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data , 2008, Nature.

[26]  Thomas A. Steitz,et al.  The involvement of RNA in ribosome function , 2002, Nature.

[27]  S. Grzesiek,et al.  Characterization of the hydrogen bond network in guanosine quartets by internucleotide 3hJNC′ and 2hJNN scalar couplings , 2000, Journal of biomolecular NMR.

[28]  Ad Bax,et al.  Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data , 2008, Journal of biomolecular NMR.

[29]  S. Beaucage,et al.  Current Protocols in Nucleic Acid Chemistry , 1999 .

[30]  R. Breaker,et al.  Riboswitches as versatile gene control elements. , 2005, Current opinion in structural biology.

[31]  H. Jane Dyson,et al.  SANE (Structure Assisted NOE Evaluation): An automated model-based approach for NOE assignment , 2001, Journal of biomolecular NMR.

[32]  Yun-Xing Wang,et al.  Periodicity in residual dipolar couplings and nucleic acid structures. , 2004, Journal of the American Chemical Society.

[33]  A. Serganov,et al.  Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. , 2004, Chemistry & biology.

[34]  A. Pardi,et al.  Comparison of alignment tensors generated for native tRNAVal using magnetic fields and liquid crystalline media , 2008, Journal of biomolecular NMR.

[35]  R. Breaker,et al.  Adenine riboswitches and gene activation by disruption of a transcription terminator , 2004, Nature Structural &Molecular Biology.

[36]  Peter V. Konarev,et al.  ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis , 2007 .

[37]  T. Cech,et al.  Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena , 1982, Cell.

[38]  C D Schwieters,et al.  Internal coordinates for molecular dynamics and minimization in structure determination and refinement. , 2001, Journal of magnetic resonance.

[39]  G. Veglia,et al.  Dipolar waves as NMR maps of protein structure. , 2002, Journal of the American Chemical Society.

[40]  D. Crothers,et al.  Nucleic Acids: Structures, Properties, and Functions , 2000 .

[41]  H M Berman,et al.  A standard reference frame for the description of nucleic acid base-pair geometry. , 2001, Journal of molecular biology.

[42]  D I Svergun,et al.  Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. , 1999, Biophysical journal.

[43]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.