Use of DNAzymes for site-specific analysis of ribonucleotide modifications

RNA

Volumn 14, Issue 1, 2008, Pages 180-187

  Hengesbach, Martin ^a   Meusburger, Madeleine ^b   Lyko, Frank ^b   Helm, Mark ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

DNAzyme; Modification; Modification enzymes; Modified nucleotide; Tandem DNAzyme

Indexed keywords

DEOXYRIBONUCLEASE; NUCLEOTIDE; OLIGORIBONUCLEOTIDE; RIBONUCLEOTIDE;

5' UNTRANSLATED REGION; ARTICLE; COOLING; DNA CLEAVAGE; ELECTROPHORESIS; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; HEATING; HYDROLYSIS; ISOTOPE LABELING; NONHUMAN; PRIORITY JOURNAL; PROTEIN MODIFICATION; QUANTITATIVE ANALYSIS; RNA CLEAVAGE; RNA TRANSCRIPTION; SENSITIVITY ANALYSIS; THIN LAYER CHROMATOGRAPHY;

BASE SEQUENCE; DNA PRIMERS; DNA, CATALYTIC; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RIBONUCLEOTIDES; RNA, TRANSFER, LYS;

EID: 38049039329     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.742708     Document Type: Article

References (32)

1. Bakin, A. and Ofengand, J. 1993. Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: Analysis by the application of a new sequencing technique. Biochemistry 32: 9754-9762.
2. Bakin, A.V. and Ofengand, J. 1998. Mapping of pseudouridine residues in RNA to nucleotide resolution. Methods Mol. Biol. 77: 297-309.
3. Behm-Ansmant, I., Massenet, S., Immel, F., Patton, J.R., Motorin, Y., and Branlant, C. 2006. A previously unidentified activity of yeast and mouse RNA:pseudouridine synthases 1 (Pus1p) on tRNAs. RNA 12: 1583-1593.
4. Brule, H., Grosjean, H., Giege, R., and Florentz, C. 1998. A pseudoknotted tRNA variant is a substrate for tRNA (cytosine-5)- methyltransferase from Xenopus laevis. Biochimie 80: 977-985.
5. Buchhaupt, M., Peifer, C., and Entian, K.D. 2007. Analysis of 2′-O-methylated nucleosides and pseudouridines in ribosomal RNAs using DNAzymes. Anal. Biochem. 361: 102-108.
6. Cairns, M.J., King, A., and Sun, L.Q. 2003. Optimization of the 10-23 DNAzyme-substrate pairing interactions enhanced RNA cleavage activity at purine-cytosine target sites. Nucleic Acids Res. 31: 2883-2889. doi: 10.1093/nar/gkg378.
7. Chen, J. and Patton, J.R. 1999. Cloning and characterization of a mammalian pseudouridine synthase. RNA 5: 409-419.
8. Cruz, R.P., Withers, J.B., and Li, Y. 2004. Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme. Chem. Biol. 11: 57-67.
9. Feldman, A.R. and Sen, D. 2001. A new and efficient DNA enzyme for the sequence-specific cleavage of RNA. J. Mol. Biol. 313: 283-294.
10. Goll, M.G., Kirpekar, F., Maggert, K.A., Yoder, J.A., Hsieh, C.L., Zhang, X., Golic, K.G., Jacobsen, S.E., and Bestor, T.H. 2006. Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 311: 395-398.
11. Grosjean, H., Motorin, Y., and Morin, A. 1998. RNA-modifying and RNA-editing enzymes: Methods for their identification. In Modification and editing of RNA (eds. H. Grosjean and R. Benne), pp. 21-46. American Society of Microbiology Press, Washington, DC.
12. Grosjean, H., Keith, G., and Droogmans, L. 2004. Detection and quantification of modified nucleotides in RNA using thin-layer chromatography. Methods Mol. Biol. 265: 357-391.
13. Guymon, R., Pomerantz, S.C., Ison, J.N., Crain, P.F., and McCloskey, J.A. 2007. Post-transcriptional modifications in the small subunit ribosomal RNA from Thermotoga maritima, including presence of a novel modified cytidine. RNA 13: 396-403.
14. Lys. J. Mol. Biol. 337: 545-560.
15. Helm, M., Brule, H., Degoul, F., Cepanec, C., Leroux, J.P., Giege, R., and Florentz, C. 1998. The presence of modified nucleotides is required for cloverleaf folding of a human mitochondrial tRNA. Nucleic Acids Res. 26: 1636-1643. doi: 10.1093/nar/26.7.1636.
16. Leu(UUR). Nucleic Acids Res. 27: 756-763. doi: 10.1093/nar/27.3.756.
17. Helm, M., Petermeier, M., Ge, B., Fiammengo, R., and Jaschke, A. 2005. Allosterically activated Diels-Alder catalysis by a ribozyme. J. Am. Chem. Soc. 127: 10492-10493.
18. Hou, Y.M., Li, Z., and Gamper, H. 2006. Isolation of a site-specifically modified RNA from an unmodified transcript. Nucleic Acids Res. 34: e21. doi: 10.1093/nar/gnj018.
19. Jeltsch, A., Nellen, W., and Lyko, F. 2006. Two substrates are better than one: Dual specificities for Dnmt2 methyltransferases. Trends Biochem. Sci. 31: 306-308.
20. Keith, G. 1995. Mobilities of modified ribonucleotides on two-dimensional cellulose thin-layer chromatography. Biochimie 77: 142-144.
21. Kuchino, Y., Hanyu, N., and Nishimura, S. 1987. Analysis of modified nucleosides and nucleotide sequence of tRNA. Methods Enzymol. 155: 379-396.
22. Kurschat, W.C., Muller, J., Wombacher, R., and Helm, M. 2005. Optimizing splinted ligation of highly structured small RNAs. RNA 11: 1909-1914.
23. Matsuyama, S., Ueda, T., Crain, P.F., McCloskey, J.A., and Watanabe, K. 1998. A novel wobble rule found in starfish mitochondria. Presence of 7-methylguanosine at the anticodon wobble position expands decoding capability of tRNA. J. Biol. Chem. 273: 3363-3368.
24. Motorin, Y. and Grosjean, H. 1999. Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: Identification of the gene and substrate specificity of the enzyme. RNA 5: 1105-1118.
25. Pomerantz, S.C. and McCloskey, J.A. 2005. Detection of the common RNA nucleoside pseudouridine in mixtures of oligonucleotides by mass spectrometry. Anal. Chem. 77: 4687-4697.
26. Saikia, M., Dai, Q., Decatur, W.A., Fournier, M.J., Piccirilli, J.A., and Pan, T. 2006. A systematic, ligation-based approach to study RNA modifications. RNA 12: 2025-2033.
27. Santoro, S.W. and Joyce, G.F. 1997. A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. 94: 4262-4266.
28. Silberklang, M., Prochiantz, A., Haenni, A.L., and Rajbhandary, U.L. 1977. Studies on the sequence of the 3′-terminal region of turnip-yellow-mosaic-virus RNA. Eur. J. Biochem. 72: 465-478.
29. Silverman, S.K. 2005. In vitro selection, characterization, and application of deoxyribozymes that cleave RNA. Nucleic Acids Res. 33: 6151-6163. doi: 10.1093/nar/gki930.
30. Tomita, K., Ueda, T., and Watanabe, K. 1999. The presence of pseudouridine in the anticodon alters the genetic code: A possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria. Nucleic Acids Res. 27: 1683-1689. doi: 10.1093/nar/27.7.1683.
31. Yu, Y.T., Shu, M.D., and Steitz, J.A. 1997. A new method for detecting sites of 2′-O-methylation in RNA molecules. RNA 3: 324-331.
32. Zhao, X. and Yu, Y.T. 2004. Detection and quantitation of RNA base modifications. RNA 10: 996-1002.