A post-labeling approach for the characterization and quantification of RNA modifications based on site-directed cleavage by DNAzymes

Methods in Molecular Biology

Volumn 718, Issue , 2011, Pages 259-270

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

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b JOHANNES GUTENBERG UNIVERSITY   (Germany)

Author keywords

Catalytic DNA; DNAzyme; Modified nucleotides; Post labeling; RNA cleavage; Thin layer chromatography

Indexed keywords

DEOXYRIBOZYME; PSEUDOURIDINE; RIBONUCLEASE; NUCLEOTIDE; RNA;

ARTICLE; CHEMICAL MODIFICATION; COMPLEX FORMATION; ENZYME PHOSPHORYLATION; HIGH TEMPERATURE; IN VITRO SELECTION; IN VITRO STUDY; ISOTOPE LABELING; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; RNA CLEAVAGE; RNA ISOLATION; RNA MODIFICATION; THIN LAYER CHROMATOGRAPHY; CHEMISTRY; HUMAN; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; CHROMATOGRAPHY, THIN LAYER; DNA, CATALYTIC; HUMANS; NUCLEOTIDES; RNA;

EID: 84855474972     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-018-8_16     Document Type: Article

References (17)

1. Zhao, X. and Y.T. Yu, Detection and quantitation of RNA base modifications. RNA, 2004. 10(6): p. 996-1002.
2. Baum, D.A. and S.K. Silverman, Deoxyribozymes: useful DNA catalysts in vitro and in vivo. Cell Mol Life Sci, 2008. 65(14): p. 2156-74.
3. Breaker, R.R. and G.F. Joyce, A DNA enzyme that cleaves RNA. Chem Biol, 1994. 1(4): p. 223-9.
4. Santoro, S.W. and G.F. Joyce, A general purpose RNA-cleaving DNA enzyme. Proc Natl Acad Sci U S A, 1997. 94(9): p. 4262-6.
5. Cairns, M.J., A. King, and L.Q. Sun, Optimisation of the 10-23 DNAzyme-substrate pairing interactions enhanced RNA cleavage activity at purine-cytosine target sites. Nucleic Acids Res, 2003. 31(11): p. 2883-9.
6. Cruz, R.P., J.B. Withers, and Y. Li, Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme. Chem Biol, 2004. 11(1): p. 57-67.
7. Buchhaupt, M., C. Peifer, and K.D. Entian, Analysis of 2¢-O-methylated nucleosides and pseudouridines in ribosomal RNAs using DNAzymes. Anal Biochem, 2007. 361(1): p. 102-8.
8. Hengesbach, M., et al., Use of DNAzymes for site-specific analysis of ribonucleotide modifications.RNA, 2008. 14(1): p. 180-7.
9. Zaborowska, Z., et al., Sequence requirements in the catalytic core of the "10-23" DNA enzyme. J Biol Chem, 2002. 277(43): p. 40617-22.
10. Zaborowska, Z., et al., Deletion analysis in the catalytic region of the 10-23 DNA enzyme.FEBS Lett, 2005. 579(2): p. 554-8.
11. Stanley, J. and S. Vassilenko, A different approach to RNA sequencing. Nature, 1978. 274: p. 87-9.
12. Helm, M., Post-transcriptional nucleotide modification and alternative folding of RNA.Nucleic Acids Res, 2006. 34(2): p. 721-33.
13. Schubert, S., et al., RNA cleaving '10-23' DNAzymes with enhanced stability and activity. Nucleic Acids Res, 2003. 31(20): p. 5982-92.
14. Vester, B., et al., LNAzymes: incorporation of LNA-type monomers into DNAzymes markedly increases RNA cleavage. J Am Chem Soc, 2002. 124(46): p. 13682-3.
15. Grosjean, H., G. Keith, and L. Droogmans, Detection and quantification of modified nucleotides in RNA using thin-layer chromatography.Methods Mol Biol, 2004. 265: p. 357-91.
16. Voigts-Hoffmann, F., et al., A methyl group controls conformational equilibrium in human mitochondrial tRNA(Lys). J Am Chem Soc, 2007. 129(44): p. 13382-3.
17. Li, J., W. Zheng, A. H. Kwon and Y. Lu. In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme. Nucleic Acids Res., 2000. 28(2): 481-8.