Preparation and crystallization of RNA

Methods in Molecular Biology

Volumn 363, Issue , 2007, Pages 239-257

  Golden, Barbara L ^a  

^a NONE

Author keywords

Heavy atom derivatives; Ribozyme; RNA; RNA crystallization; RNA purification; RNA synthesis; RNA protein interaction; T7 RNA transcription

Indexed keywords

RNA;

ARTICLE; CHEMISTRY; CONFORMATION; CRYSTALLIZATION; METHODOLOGY; SYNTHESIS; X RAY CRYSTALLOGRAPHY;

CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; NUCLEIC ACID CONFORMATION; RNA;

EID: 33847302075     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-209-2:239     Document Type: Article

References (28)

1. Anderson, A. C., Earp, B. E., and Frederick, C. A. (1996) Sequence variation as a strategy for crystallizing RNA motifs. J. Mol. Biol. 259, 696-703.
2. Correll, C. C., Wool, I. G., and Munishkin, A. (1999) The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: the structure at 1.11 Å resolution. J. Mol. Biol. 292, 275-287.
3. 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.
4. Price, S. R., Ito, N., Oubridge, C., Avis, J. M., and Nagai, K. (1995) Crystallization of RNA-protein complexes. I. Methods for the large-scale preparation of RNA suitable for crystallographic studies. J. Mol. Biol. 249, 398-408.
5. Scott, W. G., Finch, J. T., Grenfell, R., et al. (1995) Rapid crystallization of chemically synthesized hammerhead RNAs using a double screening procedure. J. Mol. Biol. 250, 327-332.
6. Hoggan, D. B., Chao, J. A., Prasad, G. S., Stout, C. D., and Williamson, J. R. (2003) Combinatorial crystallization of an RNA-protein complex. Acta Crystallogr. D. Biol. Crystallogr. 59, 466-473.
7. Pley, H. W., Flaherty, K. M., and McKay, D. B. (1994) Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature 372, 111-113.
8. Ferré-D' Amaré, 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.
9. Shields, T. P., Mollova, E., Ste Marie, L., Hansen, M. R., and Pardi, A. (1999) High-performance liquid chromatography purification of homogenous-length RNA produced by trans cleavage with a hammerhead ribozyme. RNA 5, 1259-1267.
10. Grosshans, C. A. and Cech, T. R. (1991) A hammerhead ribozyme allows synthesis of a new form of the tetrahymena ribozyme homogeneous in length with a 3' end blocked for transesterification. Nucleic Acids Res. 19, 3875-3880.
11. Milligan, J. F. and Uhlenbeck, O. C. (1989) Synthesis of small RNAs using T7 RNA polymerase. Meth. Enzymol. 180, 51-62.
12. Kao, C., Zheng, M., and Rudisser, S. (1999) A simple and efficient method to reduce nontemplated nucleotide addition at the 3 terminus of RNAs transcribed by T7 RNA polymerase. RNA 5, 1268-1272.
13. Davanloo, P., Rosenberg, A. H., Dunn, J. J., and Studier, F. W (1984) Cloning and expression of the gene for bacteriophage-T7 RNA-polymerase. Proc. Natl. Acad. Sci. USA 81, 2035-2039.
14. Li, Y., Wang, E., and Wang, Y. (1999) A modified procedure for fast purification of T7 RNA polymerase. Protein Expr. Purifi 16, 355-358.
15. Chen, C. J., Liu, Z. J., Rose, J. P., and Wang, B. C. (1999) Low-salt crystallization of T7 RNA polymerase: a first step towards the transcription bubble complex. Acta Crystallogr. D. Biol. Crystallogr. 55, 1188-1192.
16. Uhlenbeck, O. C. (1995) Keeping RNA happy. RNA 1, 4-6.
17. 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. USA 90, 7829-7833.
18. Berger, I., Kang, C. H., Sinha, N., Wolters, M., and Rich, A. (1996) A highly efficient 24-condition matrix for the crystallization of nucleic acid fragments. Acta Crystallogr. D. Biol. Crystallogr. 52, 465-468.
19. Cate, J. H. and Doudna, J. A. (1996) Metal-binding sites in the major groove of a large ribozyme domain. Structure 4, 1221-1229.
20. Cruse, W., Saludjian, P., Neuman, A., and Prange, T. (2001) Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues. Acta Crystallogr. D. Biol. Crystallogr. 57, 1609-1613.
21. Basu, S., Rambo, R. P., Strauss-Soukup, J., et al. (1998) A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nat. Struct. Biol. 5, 986-992.
22. Ennifar, E., Carpentier, P., Ferrer, J. L., Walter, P., and Dumas, P. (2002) X-rayinduced debromination of nucleic acids at the Br K absorption edge and implications for MAD phasing. Acta Crystallogr. D. Biol. Crystallogr. 58, 1262-1268.
23. Carrasco, N., Ginsburg, D., Du, Q., and Huang, Z. (2001) Synthesis of seleniumderivatized nucleosides and oligonucleotides for X-ray crystallography. Nucleosides Nucleotides Nucleic Acids 20, 1723-1734.
24. Yang, W. and Steitz, T. A. (1995) Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site. Cell 82, 193-207.
25. Horvath, M. P., Schweiker, V. L., Bevilacqua, J. M., Ruggles, J. A., and Schultz, S. C. (1998) Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA. Cell 95, 963-974.
26. Slim, G. and Gait, M. J. (1991) Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes. Nucleic Acids Res. 19, 1183-1188.
27. Moore, M. J. and Query, C. C. (2000) Joining of RNAs by splinted ligation. Meth. Enzymol. 317, 109-123.
28. 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.