Crystallographic analysis of small ribozymes and riboswitches

Methods in Molecular Biology

Volumn 848, Issue , 2012, Pages 159-184

  Lippa, Geoffrey M ^a   Liberman, Joseph A ^a   Jenkins, Jermaine L ^a   Krucinska, Jolanta ^a   Salim, Mohammad ^a   Wedekind, Joseph E ^a  

^a UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

Author keywords

Crystal screen; Purification; Riboswitches; Ribozymes; RNA; RNA synthesis; X ray crystallography

Indexed keywords

DNA; DNA DIRECTED DNA POLYMERASE BETA; RIBOZYME;

ARTICLE; BIOSYNTHESIS; CHEMISTRY; GEL CHROMATOGRAPHY; GENETICS; ION EXCHANGE; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN SYNTHESIS; RIBOSWITCH; ROBOTICS; X RAY CRYSTALLOGRAPHY;

CHROMATOGRAPHY, GEL; CRYSTALLOGRAPHY, X-RAY; DNA; DNA POLYMERASE I; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ION EXCHANGE; PROTEIN BIOSYNTHESIS; RIBOSWITCH; RNA, CATALYTIC; ROBOTICS;

EID: 84858163283     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-545-9_11     Document Type: Article

References (31)

1. Wedekind, J. E. (2011) in Met. Ions Life Sci.: Structural and Catalytic Roles of Metal Ions in RNA, eds. A. Sigel, H. Sigel, R. Sigel, Royal Society of Chemistry, London, pp. 299-345.
2. Wedekind, J. E. and McKay, D. B. (2003) Crystal structure of the leadzyme at 1. 8A resolution: metal ion binding and the implications for catalytic mechanism and allo site ion regulation. Biochemistry 42, 9554-9563. (Pubitemid 37006304)
3. Alam, S., Grum-Tokars, V., Krucinska, J., Kundracik, M. L. and Wedekind, J. E. (2005) Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn. Biochemistry 44, 14396-14408. (Pubitemid 41567448)
4. Spitale, R. C., Torelli, A. T., Krucinska, J., Bandarian, V. and Wedekind, J. E. (2009) The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain. J Biol Chem 284, 11012-11016.
5. Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S. R. and Bateman, A. (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33, D121-124. (Pubitemid 40207843)
6. Ren, J., Rastegari, B., Condon, A. and Hoos, H. H. (2005) HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. RNA 11, 1494-1504. (Pubitemid 41396919)
7. Wedekind, J. E. and McKay, D. B. (2000) Purification, crystallization, and X-ray diffraction analysis of small ribozymes. Methods Enzymol. 317, 149-168. (Pubitemid 30418084)
8. Golden, B. L., Gooding, A. R., Podell, E. R. and Cech, T. R. (1996) X-ray crystallography of large RNAs: heavy-atom derivatives by RNA engineering. RNA 2, 1295-1305. (Pubitemid 26419223)
9. Robertson, M. P. and Scott, W. G. (2008) A general method for phasing novel complex RNA crystal structures without heavy-atom derivatives. Acta Crystallogr D Biol Crystallogr D64, 738-744. (Pubitemid 351872053)
10. Keel, A. Y., Rambo, R. P., Batey, R. T. and Kieft, J. S. (2007) A general strategy to solve the phase problem in RNA crystallography. Structure 15, 761-772. (Pubitemid 47042432)
11. Beaucage, S. L. and Reese, C. B. (2009) Recent advances in the chemical synthesis of RNA. Curr Protoc Nucleic Acid Chem Chapter 2, Unit 2 16 11-31.
12. Torelli, A. T., Spitale, R. C., Krucinska, J. and Wedekind, J. E. (2008) Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme. Biochem Biophys Res Commun 371, 154-158.
13. Spitale, R. C., Volpini, R., Mungillo, M. V., Krucinska, J., Cristalli, G. and Wedekind, J. E. (2009) Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core. Biochemistry 48, 7777-7779.
14. Sinha, N. D., Biernat, J., McManus, J. and Koster, H. (1984) Polymer support oligonucleotide synthesis XVIII: use of beta-cyanoethyl-N,N- dialkylamino-/N-morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product. Nucleic Acids Res 12, 4539-4557.
15. Spitale, R. C. and Wedekind, J. E. (2009) Exploring ribozyme conformational changes with X-ray crystallography. Methods 49, 87-100.
16. Hartsel, S. A., Kitchen, D. E., Scaringe, S. A. and Marshall, W. S. (2005) RNA oligonucleotide synthesis via 5′-silyl-2′-orthoester chemistry. Methods Mol Biol 288, 33-50.
17. Ferre-D'Amare, A. R., Zhou, K. and Doudna, J. A. (1998) A general module for RNA crystallization. J Mol Biol 279, 621-631. (Pubitemid 28279469)
18. Sherlin, L. D., Bullock, T. L., Nissan, T. A., Perona, J. J., Lariviere, F. J., Uhlenbeck, O. C. and Scaringe, S. A. (2001) Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization. RNA 7, 1671-1678. (Pubitemid 33078940)
19. Milligan, J. F. and Uhlenbeck, O. C. (1989) Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol 180, 51-62. (Pubitemid 20039565)
20. Garman, E. F. and Doublie, S. (2003) Cryocooling of macromolecular crystals: optimization methods. Methods Enzymol 368, 188-216. (Pubitemid 37498349)
21. Garman, E. F. and Owen, R. L. (2006) Cryocooling and radiation damage in macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 62, 32-47.
22. Arndt, U. W. and Wonacott, A. J., The Rotation method in crystallography: Data collection from macromolecular crystals, Elsevier/North-Holland, New York, 1977.
23. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods in Enzymology 276, 307-326. (Pubitemid 27085611)
24. Adams, P. D., Afonine, P. V., Bunkoczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L. W., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C. and Zwart, P. H. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66, 213-221.
25. Torelli, A. T., Krucinska, J. and Wedekind, J. E. (2007) A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization. RNA 13, 1052-1070. (Pubitemid 46984896)
26. Emsley, P., Lohkamp, B., Scott, W. G. and Cowtan, K. (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66, 486-501.
27. Chen, V. B., Arendall, W. B., III, Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. and Richardson, D. C. (2010) MolProbity: allatom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66, 12-21.
28. Kleywegt, G. J., Harris, M. R., Zou, J. Y., Taylor, T. C., Wahlby, A. and Jones, T. A. (2004) The Uppsala Electron-Density Server. Acta Crystallogr D Biol Crystallogr 60, 2240-2249. (Pubitemid 41742776)
29. Ferre-D'Amare, A. R. and Doudna, J. A. (2000) Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module. J Mol Biol 295, 541-556.
30. Ferre-D'Amare, A. R. (2010) Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs. Methods 52, 159-167.
31. MacElrevey, C., Spitale, R. C., Krucinska, J. and Wedekind, J. E. (2007) A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme. Acta Crystallogr. D Biol. Crystallogr. 63, 812-825. (Pubitemid 46975671)