NMR solution structure determination of RNAs

Current Opinion in Structural Biology

Volumn 10, Issue 3, 2000, Pages 298-302

  Mollova, Emilia T ^a   Pardi, Arthur ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

HYDROGEN BOND; MACROMOLECULE; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; REVIEW; RNA STRUCTURE;

EID: 0034072742     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(00)00087-7     Document Type: Review

References (34)

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7. Ojennus D.D., Mitton-Fry R.M., Wuttke D.S. Induced alignment and measurement of dipolar couplings of an SH2 domain through direct binding with filamentous phage. J Biomol NMR. 14:1999;175-179. Alignment through the weak binding of an SH2 domain to Pf1 bacteriophage is investigated. It is shown that, for more positively charged proteins, alignment is obtained by a binding mechanism at low concentrations of Pf1 and the observed modest line broadening does not interfere with the accurate measurement of large residual dipolar couplings.
8. Siegal G., van Duynhoven J., Baldus M. Biomolecular NMR: recent advances in liquids, solids and screening. Curr Opin Chem Biol. 3:1999;530-536. A review of the recent developments in the biomolecular NMR field, including the measurement of residual dipolar couplings by solution NMR. The currently available media for the partial alignment of macromolecules are examined.
9. Hansen M., Hanson P., Pardi A. Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions. Methods Enzymol. 317:2000;220-240. This article provides a detailed protocol for the preparation of bacteriophage Pf1 for the partial alignment of macromolecules. The alignment properties of the phage were examined under a variety of conditions. Examples of aligning RNA and DNA molecules with phage are presented.
10. 1H distances in solution by dipolar coupling interactions. J Am Chem Soc. 120:1998;11210-11211.
11. 1H dipolar couplings is proposed. The technique is based on the analysis of peak intensities in a constant-time correlation spectroscopy (COSY) experiment.
12. α residual dipolar couplings in proteins are accurately measured from the spectrum.
13. 2 groups in proteins. Both the size and the absolute sign of the couplings are determined.
14. 1H dipolar couplings in macromolecular structure refinement. The procedure was applied to the refinement of ubiquitin and improved the precision and accuracy of the structure.
15. 13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nat Struct Biol. 4:1997;732-738.
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17. Beyer P., Varani L., Varani G. Refinement of the structure of protein-RNA complexes by residual dipolar coupling analysis. J Biomol NMR. 14:1999;149-155. This paper describes the first attempt to refine an RNA structure using dipolar coupling information. The addition of dipolar coupling constraints improved the definition of the long-range properties of RNA. Specific problems of the application of the approach to nucleic acids are discussed.
18. 2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc Natl Acad Sci USA. 94:1997;12366-12371.
19. 13C-labeled proteins. J Am Chem Soc. 120:1998;6394-6400.
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22. 1H]-HN(CO)CA, -HN(CA)CO, -HNCACB and -HN(CO)CACB experiments are presented that complete the set of TROSY-type backbone sequential assignment experiments for proteins.
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24. 2H labeled proteins. The experiments allow couplings to be measured for proteins in the 30-40 kDa molecular weight range.
25. 1H upfield component is detected. The technique is useful for measuring scalar and dipolar one-bond J couplings.
26. NN couplings. J Am Chem Soc. 120:1998;8293-8297.
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28. HN couplings and the imino proton chemical shift in an intramolecular DNA triplex were analyzed. The results are compared with the theoretically derived dependencies of these parameters on the hydrogen bond distances.
29. NN couplings are measured for the mismatched base pairs.
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31. Majumdar A., Kettani A., Skripkin E., Patel D.J. Observation of internucleotide NHN hydrogen bonds in the absence of directly detectable protons. J Biomol NMR. 15:1999;207-211. A variation of the selective (s-) HNN-COSY (correlation spectroscopy) experiment that correlates nonexchangeable protons on the acceptor base to the donor nitrogen of the hydrogen bond is described. Amino hydrogen bonds involving exchange-broadened amino protons in DNA tetrads and hexads were detected using the technique.
32. NN couplings. The experiment is demonstrated on a DNA dimer containing an A-A mismatch.
33. 15N-labeled nucleic acids. J Am Chem Soc. 122:2000;3206-3210.
34. NN scalar couplings. J Biomol NMR. 16:2000;279-289.