Rules governing the orientation of the 2'-hydroxyl group in RNA

Journal of Molecular Biology

Volumn 274, Issue 1, 1997, Pages 54-63

  Auffinger, Pascal ^a   Westhof, Eric ^a  

^a INST DE BIOL MOLEC ET CELLULAIRE   (France)

Author keywords

Anticodon; Hydration; Molecular dynamics; Tertiary interactions; tRNA

Indexed keywords

DNA A; HYDROXYL GROUP; OXYGEN; RNA; WATER;

ARTICLE; COMPUTER SIMULATION; CRYSTALLOGRAPHY; HYDRATION; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR STABILITY; PRIORITY JOURNAL; RNA STRUCTURE;

EID: 0030723027     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1370     Document Type: Article

References (55)

1. Aspanticodon hairpin: 3 ns of multiple molecular dynamics simulations. Biophys. J. 71:1996;940-954.
2. Aspanticodon hairpin. J. Mol. Biol. 269:1997;326-341.
3. Aspin aqueous solution with counterions. J. Am. Chem. Soc. 117:1995;6720-6726.
4. Auffinger P., Louise-May S., Westhof E. Hydration of C-H groups in tRNA. Farad. Discuss. 103:1996a;151-174.
5. Asp: Structuring effects of C-H.O hydrogen bonds and of long-range hydration forces. J. Am. Chem. Soc. 118:1996b;1181-1189.
6. α-H.O=C hydrogen bonds in a collagen triple helix. J. Mol. Biol. 264:1996;734-742.
7. 4′in cytosine-rich DNA. Proc. Natl Acad. Sci. USA. 93:1996;12116-12121.
8. Berman H. M., Olson W. K., Beveridge D. L., Westbrook J., Gelbin A., Demeny T., Hsieh S. H., Srinivasan A. R. The nucleic acid database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63:1992;751-759.
9. Ser. Science. 263:1994;1404-1436.
10. Biswas R., Sundaralingam M. Crystal structure of r(GUGUGUA)dC with tandem GU/UG wobble pairs with strand slippage. J. Mol. Biol. 270:1997;511-519.
11. Bolton P. H., Kearns D. R. Hydrogen bonding of the 2′-OH in RNA. Biochi. Biophys. Acta. 517:1978;329-337.
12. Cate J. H., Gooding A. R., Podell E., Zhou K. H., Golden B. L., Kundrot C. E., Cech T. R., Doudna J. A. Crystal structure of a group I ribozyme domain. Principles of RNA packing. Science. 273:1996;1678-1685.
13. 2determined by NMR. Nucl. Acids Res. 24:1996;3693-3699.
14. Darden T., York D., Pedersen L. Particle mesh Ewald: an N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:1993;10089-10092.
15. ε-H.O=C
16. Derewenda Z. S., Lee L., Derewenda U. The occurrence of C-H.O hydrogen bonds in proteins. J. Mol. Biol. 252:1995;248-262.
17. Desiraju G. R. Supramolecular synthons in crystal engineering. A new organic synthesis. Angew. Chem. Int. Ed. Engl. 34:1995;2311-2327.
18. Desiraju G. R. The C-H.O hydrogen bond: structural implications and supramolecular design. Acc. Chem. Res. 29:1996;441-449.
19. 2. J. Mol. Biol. 209:1989;459-474.
20. Eckstein F., Lilley D. M. J. Editors of Catalytic RNA. Nucleic Acids and Molecular Biology. 1996;Springer, Berlin.
21. Egli M. Structural aspects of nucleic acid analogs and antisense oligonucleotides. Angew. Chem. Int. Ed. Engl. 35:1996;1894-1909.
22. 4′on DNA conformation. Proc. Natl Acad. Sci. USA. 92:1995;180-184.
23. Egli M., Portmann S., Usman N. RNA hydration: a detailed look. Biochemistry. 35:1996;8489-8494.
24. Engh R. A., Brandstetter H., Sucher G., Eichinger A., Baumann U., Bode W., Huber R., Poll T., Rudolph R., von der Saal W. Enzyme flexibility, solvent and 'weak' interactions characterize thrombin-ligand interactions: implications for drug design. Structure. 4:1996;1353-1362.
25. Essmann U., Perera L., Berkowitz M. L., Darden T., Lee H., Pedersen L. G. A smooth particle mesh Ewald method. J. Chem. Phys. 103:1995;8577-8593.
26. Fabiola G. F., Krishnaswamy S., Nagarajan V., Pattabhi V. C-H.O hydrogen bonds in β-sheets. Acta Crystallog. sect. D. 53:1997;316-320.
27. Gesteland R. F., Atkins J. F. Editors ofThe RNA World. 1993;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
28. Jeffrey G. A., Saenger W. Hydrogen Bonding in Biological Structures. 1991;Springer-Verlag, Berlin.
29. Leonard G. A., McAuley-Hecht K., Brown T., Hunter W. N. Do C-H.O hydrogen bonds contribute to the stability of nucleic acid base pairs? Acta Crystallog. sect D. 51:1995;136-139.
30. Leroy J. L., Broseta D., Guéron M. Proton exchange and base-pair kinetics of poly(rA).poly(rU) and poly(rI).poly(rC). J. Mol. Biol. 184:1985;165-178.
31. Louise-May S., Auffinger P., Westhof E. Calculation of nucleic acid conformation. Curr. Opin. Struct. Biol. 6:1996;289-298.
32. Masquida B., Westhof E. Crystallographic structures of RNA oligoribonucleotides and ribozymes. Oxford Handbook of Nucleic Acid Structure. 1998.
33. Metzger S., Lippert B. A metalated guanine,cytosine base quartet with a novel GC pairing pattern involving H(5) of C. J. Am Chem. Soc. 118:1996;12467-12468.
34. Miller J., Kollman P. A. Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics. J. Mol. Biol. 270:1997;436-450.
35. Pearlman D. A., Kim S. H. Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data. J. Mol. Biol. 211:1990;171-187.
36. Pearlman, D. A. Case, D. A. Caldwell, J. W. Ross, W. S. Cheatham, T. E. Ferguson, D. M. Seibel, G. L. Singh, U. C. Weiner, P. K. Kollman, P. A. 1994, AMBER 4.1, San Francisco, California.
37. Pley H. M., Flaherty K. M., McKay D. B. Three-dimensional structure of a hammerhead ribozyme. Nature. 372:1994;68-74.
38. Quigley G. J., Rich A. Structural domains of transfer RNA molecules. Science. 194:1976;796-806.
39. Rould M. A., Perona J. J., Steitz T. A. Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature. 352:1991;213-218.
40. Saenger W. Editor of Principles of Nucleic Acid Structure. Cantor C. R. Springer Advanced Text in Chemistry. 1984.
41. Schindelin H., Zhang M., Bald R., Fürste J. P., Erdman V. A., Heinemann U. Crystal structure of an RNA dodecamer containing the Escherichia coli Shine-Dalgarno sequence. J. Mol. Biol. 249:1995;595-603.
42. Scott W. G., Murray J. B., Arnold J. R. P., Stoddard B. L., Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science. 274:1996;2065-2069.
43. Singh S. B., Kollman P. A. Understanding the thermodynamic stability of an RNA hairpin and its mutant. Biophys. J. 70:1996;1940-1948.
44. Steiner T. Water which apparently accept no hydrogen bonds are systematically involved in C-H.O interactions. Acta Crystallog. sect. D. 51:1995;93-97.
45. Steiner T. C-H.O hydrogen bonding in crystals. Crystallog Rev. 6:1996;1-57.
46. 12coenzyme at 15 K is stabilized by C-H.O acceptor hydrogen bonds. Acta Crystallog. sect. D. 49:1993a;592-593.
47. Steiner T., Saenger W. Role of C-H···O hydrogen bonds in the coordination of water molecules. Analysis of neutron diffraction data. J. Am. Chem. Soc. 115:1993b;4540-4547.
48. Takahara P. M., Frederick C. A., Lippard S. J. Crystal structure of the anticancer drug cisplatin bound to duplex DNA. J. Am. Chem. Soc. 118:1996;12309-12321.
49. Taylor R., Kennard O. Crystallographic evidence for the existence of C-H.O, C-H.N and C-H.Cl hydrogen bonds. J. Am. Chem. Soc. 104:1982;5063-5070.
50. Wahl C. M., Sundaralingam M. C-H.O hydrogen bonding in biology. Trends Biochem. Sci. 22:1997;97-102.
51. Wahl M. C., Ban C., Sekharudu C., Ramakrishnan B., Sundaralingam M. Structure of the purine-pyrimidine alterning RNA double helix, r(GUAUAUA)d(C) with a 3′-terminal deoxy residue. Acta Crystallog. sect. D. 52:1996a;655-667.
52. Wahl M. C., Rao S. T., Sundaralingam M. The structure of r(UUCGCG) has a 5′-UU-overhang exhibiting Hoogsteen-like trans U.U base pairs. Nature Struct. Biol. 3:1996b;24-31.
53. Westhof E., Beveridge D. L. Hydration of nucleic acids. Franks F. Water Science Reviews 5. 1990;Cambridge University Press, Cambridge.
54. Westhof E., Dumas P., Moras D. Crystallographic refinement of yeast aspartic acid transfer RNA. J. Mol. Biol. 184:1985;119-145.
55. Westhof E., Dumas P., Moras D. Hydration of transfer RNA molecules: a crystallographic study. Biochimie. 70:1988;145-165.