Local RNA structural changes induced by crystallization are revealed by SHAPE

RNA

Volumn 13, Issue 4, 2007, Pages 536-548

  Vicens, Quentin ^a   Gooding, Anne R ^a   Laederach, Alain ^b   Cech, Thomas R ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

Chemical probing; Crystallization; Structure mapping; X ray crystallography

Indexed keywords

ACYLATION; ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; CRYSTALLIZATION; IN VITRO SELECTION; INTRON; PRIORITY JOURNAL; RNA ANALYSIS; RNA STRUCTURE; STRUCTURE ANALYSIS; TETRAHYMENA THERMOPHILA; X RAY CRYSTALLOGRAPHY;

ACYLATION; ANIMALS; BASE PAIRING; BASE SEQUENCE; BUFFERS; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; INTRONS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA; RNA, CATALYTIC; RNA, PROTOZOAN; SOLUTIONS; TETRAHYMENA THERMOPHILA;

TETRAHYMENA THERMOPHILA;

EID: 33947725371     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.400207     Document Type: Article

References (51)

1. Adams, P.L., Stahley, M.R., Gill, M.L., Kosek, A.B., Wang, J., and Strobel, S.A. 2004. Crystal structure of a group I intron splicing intermediate. RNA 10: 1867-1887.
2. Altona, C. and Sundaralingam, M. 1972. Conformational-analysis of sugar ring in nucleosides and nucleotides - New description using the concept of pseudorotation. J. Am. Chem. Soc. 94: 8205-8212.
3. Anderson, A.C., Earp, B.E., and Frederick, C.A. 1996. Sequence variations as a strategy for crystallizing RNA motifs. J. Mol. Biol. 259: 696-703.
4. Auffinger, P. and Westhof, E. 1997. Rules governing the orientation of the 2′-hydroxyl group in RNA. J. Mol. Biol. 274: 54-63.
5. Badorrek, C.S. and Weeks, K.M. 2006. Architecture of a γ retroviral genomic RNA dimer. Biochemistry 45: 12664-12672.
6. Badorrek, C.S., Gherghe, C.M., and Weeks, K.M. 2006. Structure of an RNA switch that enforces stringent retroviral genomic RNA dimerization. Proc. Natl. Acad. Sci. 103: 13640-13645.
7. Ban, N., Nissen, P., Hansen, J., Moore, P.B., and Steitz, T.A. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289: 905-920.
8. Batey, R.T., Sagar, M.B., and Doudna, J.A. 2001. Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle. J. Mol. Biol. 307: 229-246.
9. Batey, R.T., Gilbert, S.D., and Montange, R.K. 2004. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432: 411-415.
10. Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., et al. 1998. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54: 905-921.
11. Cate, J.H., Gooding, A.R., Podell, E., Zhou, K., Golden, B.L., Kundrot, C.E., Cech, T.R., and Doudna, J.A. 1996. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273: 1678-1684.
12. Chamberlin, S.I. and Weeks, K.M. 2000. Mapping local nucleotide flexibility by selective acylation of 2′-amine substituted RNA. J. Am. Chem. Soc. 122: 216-224.
13. Chen, Y., Fender, J., Legassie, J.D., Jarstfer, M.B., Bryan, T.M., and Varani, G. 2006. Structure of stem-loop IV of Tetrahymena telomerase RNA. EMBO J. 25: 3156-3166.
14. Asp. 1. Structure determination. Acta Crystallogr. B 42: 272-280.
15. Das, R., Laederach, A., Pearlman, S.M., Herschlag, D., and Altman, R.B. 2005. SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid foot-printing experiments. RNA 11: 344-354.
16. Doudna, J.A., Grosshans, C., Gooding, A., and Kundrot, C.E. 1993. Crystallization of ribozymes and small RNA motifs by a sparse matrix approach. Proc. Natl. Acad. Sci. 90: 7829-7833.
17. Efron, B. 1979. 1977 Rietz Lecture - Bootstrap methods - Another look at the jackknife. Ann. Stat. 7: 1-26.
18. Efron, B. and Tibshirani, R.J. 1993. An introduction to the bootstrap. Chapman & Hall/CRC, Boca Raton, FL.
19. Ferré-D'Amaré, A.R., Zhou, K.H., and Doudna, J.A. 1998. Crystal structure of a hepatitis δ virus ribozyme. Nature 395: 567-574.
20. Gesteland, R.F., Cech, T.R., and Atkins, J.F. 2005. The RNA world. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
21. Gherghe, C.M., Krahn, J.M., and Weeks, K.M. 2005. Crystal structures, reactivity and inferred acylation transition states for 2′-amine substituted RNA. J. Am. Chem. Soc. 127: 13622-13628.
22. Golden, B.L., Podell, E.R., Gooding, A.R., and Cech, T.R. 1997. Crystals by design: A strategy for crystallization of a ribozyme derived from the Tetrahymena group I intron. J. Mol. Biol. 270: 711-723.
23. Golden, B.L., Kim, H., and Chase, E. 2005. Crystal structure of a phage Twort group I ribozyme-product complex. Nat. Struct. Mol. Biol. 12: 82-89.
24. Guex, N. and Peitsch, M.C. 1997. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18: 2714-2723.
25. Guo, F. and Cech, T.R. 2002. Evolution of Tetrahymena ribozyme mutants with increased structural stability. Nat. Struct. Biol. 9: 855-861.
26. Guo, F., Gooding, A.R., and Cech, T.R. 2004. Structure of the Tetrahymena ribozyme: Base triple sandwich and metal ion at the active site. Mol. Cell 16: 351-362.
27. Guo, F., Gooding, A.R., and Cech, T.R. 2006. Comparison of crystal structure interactions and thermodynamics for stabilizing mutations in the Tetrahymena ribozyme. RNA 12: 387-395.
28. Juneau, K. and Cech, T.R. 1999. In vitro selection of RNAs with increased tertiary structure stability. RNA 5: 1119-1129.
29. Juneau, K., Podell, E., Harrington, D.J., and Cech, T.R. 2001. Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions. Structure 9: 221-231.
30. Kim, S.H., Suddath, F.L., Quigley, G.J., McPherson, A., Sussman, J.L., Wang, A.H., Seeman, N.C., and Rich, A. 1974. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 185: 435-440.
31. Leontis, N.B. and Westhof, E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7: 499-512.
32. Mathews, D.H. and Turner, D.H. 2006. Prediction of RNA secondary structure by free energy minimization. Curr. Opin. Struct. Biol. 16: 270-278.
33. Merino, E.J., Wilkinson, K.A., Coughlan, J.L., and Weeks, K.M. 2005. RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc. 127: 4223-4231.
34. Moras, D., Dock, A.C., Dumas, P., Westhof, E., Romby, P., Ebel, J.P., and Giegé, R. 1986. Anticodon-anticodon interaction induces conformational changes in tRNA: Yeast tRNAAsp, a model for tRNA-mRNA recognition. Proc. Natl. Acad. Sci. 83: 932-936.
35. Murphy, F.L. and Cech, T.R. 1993. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry 32: 5291-5300.
36. Ortoleva-Donnelly, L., Szewczak, A.A., Gutell, R.R., and Strobel, S.A. 1998. The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. RNA 4: 498-519.
37. Potterton, E., Briggs, P., Turkenburg, M., and Dodson, E. 2003. A graphical user interface to the CCP4 program suite. Acta Crystallogr. D 59: 1131-1137.
38. Richards, F.M. 1974. The interpretation of protein structures: Total volume, group volume distributions and packing density. J. Mol. Biol. 82: 1-14.
39. Robertus, J.D., Ladner, J.E., Finch, J.T., Rhodes, D., Brown, R.S., Clark, B.F., and Klug, A. 1974. Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature 250: 546-551.
40. Rupert, P.B. and Ferré-D'Amaré, A.R. 2001. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410: 780-786.
41. Schluenzen, F., Tocilj, A., Zarivach, R., Harms, J., Gluehmann, M., Janell, D., Bashan, A., Bartels, H., Agmon, I., Franceschi, F., et al. 2000. Structure of functionally activated small ribosomal subunit at 3.3 Å resolution. Cell 102: 615-623.
42. Scott, W.G., Finch, J.T., Grenfell, R., Fogg, J., Smith, T., Gait, M.J., and Klug, A. 1995. Rapid crystallization of chemically synthesized hammerhead RNAs using a double screening procedure. J. Mol. Biol. 250: 327-332.
43. Stahley, M.R. and Strobel, S.A. 2005. Structural evidence for a twometal-ion mechanism of group I intron splicing. Science 309: 1587-1590.
44. Stout, C.D., Mizuno, H., Rubin, J., Brennan, T., Rao, S.T., and Sundaralingam, M. 1976. Atomic coordinates and molecularconformation of yeast phenylalanyl transfer-RNA-Independent investigation. Nucleic Acids Res. 3: 1111-1123.
45. Sundaralingam, M., Stout, C.D., Mizuno, H., Rubin, J., Rao, S.T., Mallikarjunan, M., and Brennan, T. 1975. Structure of yeast phenylalanine transfer-RNA. Acta Crystallogr. A 31: S39.
46. Thore, S., Leibundgut, M., and Ban, N. 2006. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312: 1208-1211.
47. Vicens, Q. and Westhof, E. 2001. Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site. Structure 9: 647-658.
48. Westhof, E., Dumas, P., and Moras, D. 1985. Crystallographic refinement of yeast aspartic-acid transfer-RNA. J. Mol. Biol. 184: 119-145.
49. Asp transcripts. J. Am. Chem. Soc. 127: 4659-4667.
50. Wilkinson, K.A., Merino, E.J., and Weeks, K.M. 2006. Selective 2́-hydroxyl acylation analyzed by primer extension (SHAPE): Quantitative RNA structure analysis at single nucleotide resolution. Nature Protocols 1: 1610-1616.
51. Wimberly, B.T., Brodersen, D.E., Clemons Jr., W.M., Morgan-Warren, R.J., Carter, A.P., Vonrhein, C., Hartsch, T., and Ramakrishnan, V. 2000. Structure of the 30S ribosomal subunit. Nature 407: 327-339.