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Nat Methods. 2014 Apr;11(4):413-6. doi: 10.1038/nmeth.2876. Epub 2014 Mar 2.

Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts.

Author information

1
Biophysics Program, Stanford University, Stanford, California, USA.
2
Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany.
3
Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, USA.
4
1] Department of Biochemistry, University of Oxford, Oxford, UK. [2] Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland.
5
Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
6
Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA.
7
Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.
8
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
9
Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland.
10
Department of Chemistry, University of Rochester, Rochester, New York, USA.
11
1] Biophysics Program, Stanford University, Stanford, California, USA. [2] Department of Biochemistry, Stanford University, Stanford, California, USA. [3] Department of Physics, Stanford University, Stanford, California, USA.

Abstract

Structured noncoding RNAs underlie fundamental cellular processes, but determining their three-dimensional structures remains challenging. We demonstrate that integrating ¹H NMR chemical shift data with Rosetta de novo modeling can be used to consistently determine high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 'blind' targets, chemical-shift Rosetta for RNA (CS-Rosetta-RNA) recovered experimental structures with high accuracy (0.6-2.0 Å all-heavy-atom r.m.s. deviation) in 18 cases.

PMID:
24584194
PMCID:
PMC3985481
DOI:
10.1038/nmeth.2876
[Indexed for MEDLINE]
Free PMC Article

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