J-coupling restraints in RNA structure determination

Accounts of Chemical Research

Volumn 32, Issue 7, 1999, Pages 614-623

  Marino, John P ^a   Schwalbe, Harald ^a   Griesinger, Christian ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; RNA STRUCTURE;

EID: 0032795253     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar9600392     Document Type: Article

References (57)

1. Karplus, M. J. Chem. Phys. 1959, 30, 11.
2. Altona, C. Conformation Analysis of Nucleic Acids. Determination of Backbone Geometry of Single-helical RNA and DNA in Aqueous Solution. Recl. Trav. Chim. Pays-Bas 1982, 101, 413-433.
3. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1988.
4. 13C-Labeled Extra-Stable Hairpin. J. Am. Chem. Soc. 1994, 116, 5823-5831.
5. 13C Spin-Coupling Constants to Assess Furanose and N-glycoside Bond Conformations. J. Am. Chem. Soc. 1990, 112, 7373-81.
6. Hines, J. V.; Varani, G.; Landry, S. M.; Tinoco, I. J. The stereospecific assignment of H5′ and H5″ in RNA using the sign of two-bond carbon-proton scalar couplings. J. Am. Chem. Soc. 1993, 115, 11002-3.
7. Varani, G.; Tinoco, I., Jr. Carbon Assignments and Heteronuclear Coupling Constants for an RNA Oligonucleotide from Natural Abundance 13C-1H Correlated Experiments. J. Am. Chem. Soc. 1991, 113, 9349-9354.
8. 1H Spin-Coupling Constants in Aldopyranoside Rings - Effect of Conformation on Coupling Magnitude. J. Am. Chem. Soc. 1995, 117, 8645-8650.
9. Davies, D. B.; Rajani, P.; MacCoss, M.; Danyluk, S. S. Determination of the Karplus Relationships for the C-2, H-1′ and C-6, H-1′ Vicinal Coupling Paths of Uridine Derivatives. Magn. Reson. Chem. 1985, 23, 72-77.
10. 15N Labeled DNA Oligonucleotides. Magn. Reson. Chem. 1997, 34, 177-186.
11. 13C labeled RNA, J. Am. Chem. Soc. 1996, 118, 4388-4395.
12. 31P NMR of DNA. Methods Enzymol. 1992, 211, 254-86.
13. Giessner-Prettre, C.; Pullman, B. Quantum Mechanical Calculations of NMR Chemical Shifts in Nucleic Acids. Q. Rev. Biophys. 1987, 20, 113-172.
14. Varani, G.; Cheong, C.; Tinoco, I. J. Structure of an unusually stable RNA hairpin. Biochemistry 1991, 30, 3280-9.
15. Müller, L. P. E. COSY, A Simple Alternative to E. COSY. J. Magn. Reson. 1987, 72, 191-196.
16. Batey, R. T.; Inada, M.; Kujawinski, E.; Puglisi, J. D.; Williamson, J. R. Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA. Nucleic Acids Res. 1992, 20, 4515-23.
17. 15N labelled RNAs for Heteronuclear Multi-dimensional NMR Studies. Nucleic Acids Res. 1992, 20, 4507-13.
18. 13C Labeled RNA and DNA monomers for the Solid Phase and Template Controlled Enymatic synthesis of DNA and RNA Oligomers. Tetrahedron Lett. 1994, 35, 6649-52.
19. 13C-Labeled Molecules. J. Magn. Reson. 1992, 75, 426-434.
20. 13C-labeled oligonucleotides. J. Biomol. NMR 1994, 4, 631-44.
21. 13C-labeled RNA by HCC-TOCSY-CCH-ECOSY. J. Am. Chem. Soc. 1995, 117, 7251-7252.
22. Glaser, S.; Schwalbe, H.; Marino, J. P.; Griesinger, S. Directed TOCSY, a Method for Selection of Directed Correlations by Optimal Combinations of Isotropic and Longitudinal Mixing. J. Magn. Reson. 1996, B112, 160-180.
23. Griesinger, C.; Sørensen, O. W.; Ersnt, R. R. Two-Dimensional Correlation of Connected NMR Transitions. J. Am. Chem. Soc. 1985, 107, 6394-6396.
24. Griesinger, C.; Sørensen, O. W.; Ernst, R. R. Practical Aspects of the E. COSY Technique. Measurement of Scalar Spin-Spin Coupling Constants in Peptides. J. Magn. Reson. 1987, 75, 474-492.
25. Bax, A.; Vuister, G. W.; Grzesiek, S.; Delaglio, F.; Wang, A. C.; Tschudin, R.; Zhu, G. Measurement of Homonuclear and Heteronuclear J-Couplings from Quantitative J-Correlation. Methods Enzymol. 1994, 239 79-105.
26. Zhu, G.; Live, D.; Bax, A. Analysis of Sugar Puckers and Glycosidic Torsion Angles in a DNA G-Tetrad Structure by Heteronuclear Three-Bond J Coupling. J. Am. Chem. Soc. 1994, 116, 8370-8371.
27. 1H Resonances in Oligonucleotides by Two-dimensional NMR Spectroscopy. FEBS 1986, 203, 94-98.
28. 3J-(H,P) Coupling Constants in Nucleotide Oligomers with FIDS-HSQC. J. Biomol. NMR 1993, 3, 479-486.
29. 13C. J. Am. Chem. Soc. 1993, 115, 5334-5335.
30. 31P J coupling constants in Isotopically Labeled RNA. FEBS Lett. 1995, 362, 156-60.
31. Hoogstraten, C.; Pardi, A. Measuring of Carbon-Phosphorus J Coupling Constants in RNA using Spin-Echo Difference Constant Time HCCH-COSY. J. Magn. Reson. 1998, 133, 236-240.
32. 3J(C4′i,-Pi+1) in Oligonucleotides. J. Biomol. NMR 1998, 12, 223-230.
33. 31P) and Two-Dimensional HeteroTOCSY. J. Am. Chem. Soc. 1994, 116, 4983-4984.
34. 31P Experiment: Sequential Through-Bond Correlation of Ribose Protons and Intervening Phosphorus along the RNA Oligonucleotide Backbone. J. Am. Chem. Soc. 1994, 116, 6472-3.
35. van Wijk, J.; Huckriede, B. D.; Ippel, J. H.; Altona, C. Furanose Sugar Conformation in DNA from NMR Coupling Constants. Methods Enzymol. 1992, 211, 286-306.
36. Lankhorst, P. P.; Haasnoot, C. A.; Erkelens, C.; Westerink, H. P.; van der Marel, G. A.; van, B., J. H.; Altona, C. Carbon-13 NMR in conformational analysis of nucleic acid fragments. 4. The torsion angle distribution about the C3′-O3′ bond in DNA constituents. Nucleic Acids Res. 1985, 13, 927-42.
37. C-C-O-P to Torsion Angle. Tetrahedron Lett. 1995, 36, 1949-1952.
38. Haasnoot, C. A.; de Leeuw, F. A. A. M.; Altona, C. The relationship between proton-proton NMR coupling constants and substituent electronegativities. I, an empirical generalization of the Karplus equation. Tetrahedron 1980, 36, 2783-2792.
39. Tvaroska, I.; Hricovini, M.; Pettakova, E. An Attempt to Derive a New Karplus-Type Equation of Vicinal Proton Carbon Coupling Constants for C-O-C-H Segments of Bonded Atoms. Carbohydr. Res. 1989, 189, 359-362.
40. 1H Spin-coupling Constants in the β-D-Ribofuranosyl Ring: Effect of Ring Conformation on Coupling Magnitudes. J. Am. Chem. Soc. 1996, 118, 1413-1425.
41. Lankhorst, P. P.; Haasnoot, C. A.; Erkelens, C.; Altona, C. Carbon-13 NMR in conformational analysis of nucleic acid fragments. 2. A reparametrization of the Karplus equation for vicinal NMR coupling constants in CCOP and HCOP fragments. J. Biomol. Struct. Dyn. 1984, 1, 1387-405.
42. Mooren, M. M.; Wijmenga, S. S.; van, d. M. G.; van, B. J.; Hilbers, C. W. The solution structure of the circular trinucleotide cr(GpGpGp) determined by NMR and molecular mechanics calculation. Nucleic Acids Res. 1994, 22, 2658-66.
43. Wüthrich, K. NMR of Proteins and Nucleic Acids; Wiley: New York, 1986.
44. Cavanagh, J.; Fairbrother, W.; Palmer, A.; Skelton, N. Protein NMR Spectroscopy: Principles and Practice; Academic Press, Inc.: New York, 1995.
45. Varani, G.; Aboul-ela, F.; Allain, F. H.-T. NMR Investigation of RNA Structure. Prog. Nucl. Reson. Spectrosc. 1996, 29, 51-127.
46. Wijmenga, S. S.; Mooren, M. M. W.; Hilbers, C. W. In NMR of Macromolecules, A Practical Approach; Roberts, G. C. K., Ed.; Oxford University Press: 1993; p 217.
47. Chang, K.; Varani, G. Nucleic Acids Structure and Recognition. Nat. Struct. Biol. 1997, 4, 854-858.
48. Ramos, A.; Gubser, C.; Varani, G. Recent Solution Structures of RNA and its Complexes with Drugs, peptides and proteins. Curr. Opin. Struct. Biol. 1997, 7, 317-323.
49. Uhlenbeck, O.; Pardi, A.; Feigon, J. RNA Structure Comes of Age. Cell 1997, 90, 833-840.
50. Allain, F. H.-T.; Varani, G. Structure of the P1 Helix from Group I Self-splicing Introns. J. Mol. Biol. 1995, 250, 333-353.
51. Allain, F. H.-T.; Varani, G. How Accurately and precisely can RNA structure be determined by NMR. J. Mol. Biol. 1997, 267, 338-351.
52. Schmitz, U.; Kumar, A.; James, T. L. Dynamic Interpretation of NMR Data-Molecular-Dynamics with Weighted Time-Averaged Restraints and Ensembe R-factor. J. Am. Chem. Soc. 1992, 114, 10654-10656.
53. Pearlman, D. A. How well do time-average J-coupling restraints work? J. Biomol. NMR 1994, 4, 279-299.
54. Reif, B.; Hennig, M.; Griesinger, C. Direct Measure of Angles Between Bond Vectors in High-Resolution NMR. Science 1997, 276, 1230-1233.
55. Tolman, J.; Flanagan, J.; Kennedy, M.; Prestegard, J. Nuclear Magnetic Dipole Interactions in Field-Oriented Proteins: Information for Structure Determination in Solution. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 9279-9283.
56. 13C Couplings in the Structure Determination of Magnetically Oriented Macromolecules in Solution. Nat. Struct. Biol. 1997, 4, 732-738.
57. Tjandra, N.; Bax, A. Direct Measurement of Distance and Angles in Biomolecules by NMR in a Dilute Liquid Crystalline Medium. Science 1997, 278, 1111-1114.