Sequence-function relationships provide new insight into the cleavage site selectivity of the 8-17 RNA-cleaving deoxyribozyme

Nucleic Acids Research

Volumn 36, Issue 5, 2008, Pages 1472-1481

  Schlosser, Kenny ^a   Gu, Jimmy ^a   Sule, Lauren ^a   Li, Yingfu ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; DEOXYRIBOZYME; DINUCLEOTIDE; DNA; GUANINE; RNA; TYROSINE;

ARTICLE; CONTROLLED STUDY; ENZYME ACTIVE SITE; GENE MUTATION; GENETIC VARIABILITY; IN VITRO STUDY; NUCLEIC ACID STRUCTURE; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA CLEAVAGE; SEQUENCE ANALYSIS;

BASE SEQUENCE; CATALYSIS; DNA, CATALYTIC; KINETICS; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; RNA; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 41149095145     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm1175     Document Type: Article

References (49)

1. 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.
2. Purtha,W.E., Coppins,R.L., Smalley,M.K. and Silverman,S.K. (2005) General deoxyribozyme-catalyzed synthesis of native 3′-5′ RNA linkages. J. Am. Chem. Soc., 127, 13124-13125.
3. Wang,Y, and Silverman,S.K. (2005) Directing the outcome of deoxyribozyme selections to favor native 3′-5′ RNA ligation. Biochemistry, 44, 3017-3023.
4. Liu,J. and Lu,Y. (2003) A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticies. J. Am. Chem. Soc. 125, 6642-6643.
5. Chiurnan,W. and Li,Y. (2007) Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates. Nucleic Acids Res., 35, 401-405.
6. Sando,S., Sasaki,T., Kanatani,K. and Aoyama,Y. (2003) Amplified nucleic acid sensing using programmed self-cleaving DNAzyme. J. Am. Chem. Soc., 125, 15720-15721.
7. Stojanovic,M.N., Mitchell,T.E. and Stefanovic,D. (2002) Deoxyribozyme-based logic gates. J. Am. Chem. Soc., 124, 3555-3561.
8. Stojanovic,M.N. and Stefanovic,D. (2003) Deoxyribozyme-based half-adder. J. Am. Chem. Soc., 125, 6673-6676.
9. Stojanovic,M.N., Semova,S., Kolpashchikov,D., Macdonald,J., Morgan,C. and Stefanovic,D. (2005) Deoxyribozyme-based ligase logic gates and their initial circuits. J. Am. Chem. Soc., 127, 6914-6915.
10. Vlassov,A.V., Ilves,H. and Johnston,B.H. (2006) Inhibition of hepatitis C IRES-mediated -gene expression by 8-17 deoxyribozymes in human tissue culture cells. Dokl. Biochem. Biophys., 410, 257-259.
11. Chakraborti,S. and Banerjea,A.C. (2003) Inhibition of HIV-1 gene expression by novel DNA enzymes targeted to cleave HIV-1 TAR RNA: potential effectiveness against all HIV-1 isolates. Mol. Ther., 7, 817-826.
12. Chakraborti,S. and Banerjea,A.C. (2003) Identification of cleavage sites in the HIV-1 TAR RNA by 10-23 and 8-17 catalytic motif containing DNA enzymes. Biomacromolecules, 4, 568-571.
13. Kankia,B.I. (2006) A real-time assay for monitoring nucleic acid cleavage by quadruplex formation. Nucleic Acids Res., 34, e14l.
14. Liu,Y. and Sen,D. (2004) Light-regulated catalysis by an RNA-cleaving deoxyribozyme. J. Mol. Biol., 341, 887-892.
15. Flynn-Charlebois,A., Prior,T.K., Hoadley,K.A. and Silverman,S.K. (2003) In vitro evolution of an RNA-cleaving DNA enzyme into an RNA ligase switches the selectivity from 3′-5′ to 2′-5′. J. Am. Chem. Soc., 125, 5346-5350.
16. Yim,T.J., Liu,J., Lu,Y., Kane,R.S. and Dordick,J.S. (2005) Highly active and stable DNAzyme-carbon nanotube hybrids. J. Am. Chem. Soc., 127, 12200-12201.
17. Ferrari,D. and Peracchi,A. (2002) A continuous kinetic assay for RNA-cleaving deoxyribozymes, exploiting ethidium bromide as an extrinsic fluorescent probe. Nucleic Acids Res. 30, e112.
18. Wernette,D.P., Swearingen,C.B., Cropek,D.M., Lu,Y., Sweedler,J.V. and Bohn,P.W. (2006) Incorporation of a DNAzyme into Au-coated nanocapillary array membranes with an internal standard for Pb(ii) sensing. Analyst 131, 41-47.
19. Pei,R., Taylor,S.K., Stefanovic,D., Rudchenko,S., Mitchell,T.E. and Stojanovic,M.N. (2006) Behavior of polycatalytic assemblies in a substrate-displaying matrix. J. Am. Chem. Soc., 128, 12693-12699
20. Wang,D.Y., Lai,B.H., Feldman,A.R. and Sen,D. (2002) A general approach for the use of oligonucleotide effectors to regulate the catalysis of RNA-cleaving ribozymes and DNAzymes. Nucleic Acids Res., 30, 1735-1742.
21. Wang,D.Y., Lai,B.H. and Sen,D. (2002) A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes. J. Mol. Biol., 318, 33-43.
22. Bonaccio,M., Credali,A. and Peracchi,A. (2004) Kinetic and thermodynamic characterization of the RNA-cleaving 8-17 deoxyribozyme. Nucleic Acids Res., 32, 916-925.
23. Brown,A.K., Li,J., Pavot,C.M. and Lu,Y. (2003) A lead-dependent DNAzyme with a two-step mechanism. Biochemistry, 42, 7152-7161.
24. Li,J., Zheng,W., Kwon,A.H. and Lu,Y. (2000) In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme. Nucleic Acids Res., 28, 481-488.
25. Peracchi,A., Bonaccio,M. and Clerici,M. (2005) A mutational analysis of the 8-17 deoxyribozyme core. J. Mol. Biol., 352, 783-794.
26. Kim,H.K., Liu,J., Li,J., Nagraj,N., Li,M., Pavot,C.M. and Lu,Y. (2007) Metal-dependent global folding and activity of the 8-17 DNAzyme studied by fluorescence resonance energy transfer. J. Am. Chem. Soc., 129, 6896-6902.
27. Liu,J. and Lu,Y. (2002) FRET study of a trifluorophore-labeled DNAzyme. J. Am. Chem. Soc., 124, 15208-15216.
28. Leung,E.K. and Sen,D. (2007) Electron hole flow patterns through the-RNA-cleaving 8-17 deoxyribozyme yield unusual information about its structure and folding. Chem. Biol., 14, 41-51.
29. Kim,H.K., Rasnik,I., Liu,J., Ha,T. and Lu,Y. (2007) Dissecting metal ion-dependent fording and catalysis of a single DNAzyme. Nat. Chem. Biol., 3, 763-768.
30. Peracchi,A. (2000) Preferential activation of the 8-17 deoxyribozyme by Ca(2+) ions. Evidence-for the identity of 8-17 with the catalytic domain of the Mg5 deoxyribozyme J. Biol. Chem., 275, 11693-11697.
31. Faulhammer,D. and Famulok,M. (1996) The Ca2+ ion as a cofactor for a novel RNA-cleaving deoxyribozyme. Angew. Chem. Int. Ed. Engl., 35, 2809-2813.
32. Schlosser,K. and Li,Y. (2004) Tracing sequence diversity change of RNA-cleaving deoxyribozymes under increasing selection pressure during in vitro selection. Biochemistry, 43, 9695-9707.
33. Santoro,S.W. and Joyce,G.F. (1997) A general purpose RNA-cleaving DNA enzyme. Proc. Natl Acad. Sci. USA, 94, 4262-4266.
34. Cruz,R.P., Withers,J.B. and Li,Y. (2004) Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme. Chem. Biol., 11, 57-67.
35. Zaborowska,Z., Furste,J.P., Erdmann,V.A. and Kurreck,J. (2002) Sequence requirements in the catalytic core of the "10-23" DNA enzyme. J. Biol. Chem., 277, 40617-40622.
36. Li,Y. and Breaker,R.R. (1999) Kinetics for specific base catalysis of RNA degradation by transesterification involve the 2′-hydroxyl group. J. Am. Chem. Soc., 121, 5364-5372.
37. Schlosser,K., Lam,J.C. and Li,Y. (2006) Characterization of long RNA-cleaving deoxyribozymes with short catalytic cores: The effect of excess sequence elements on the outcome of in vitro selection. Nucleic Acids Res., 34, 2445-2454.
38. Hertel,K.J., Pardi,A., Uhlenbeck,O.C., Koizumi,M., Ohtsuka,E., Uesugi,S., Cedergren,R., Eckstein,F., Gerlach,W.L. et al. (1992) Numbering system for the hammerhead. Nucleic Acids Res., 20, 3252.
39. Cairns,M.J., King,A. and Sun,L.Q. (2003) Optimisation of the 10-23 DNAzyme-substrate pairing interactions enhanced RNA cleavage activity at purine-cytosine target sites. Nucleic Acids Res., 31, 2883-2889.
40. Curtis,E.A. and Bartel,D.P. (2005) New catalytic structures from an existing ribozyme. Nat. Struct. Mol. Biol., 12, 994-1000.
41. Schlosser,K. and Li,Y. (2005) Diverse evolutionary trajectories characterize a community of RNA-cleaving deoxyribozymes: A case study into the population dynamics of in vitro selection. J. Mol. Evol., 61, 192-206.
42. 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.
43. Ferre-D'Amare,A.R. and Doudna,J.A. (1996) Use of cis- and trans-ribozymes to remove 5′ and 3′ heterogeneities from milligrams of in vitro transcribed RNA. Nucleic Acids Res., 24, 977-978.
44. Lapham, J. and Crothers,D.M. (1996) RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation. RNA, 2, 289-296.
45. Knight,R. and Yarus,M. (2003) Finding specific RNA motifs: Function in a zeptomole world? RNA, 9, 218-230.
46. Knight,R., De Sterck,H., Markel,R., Smit,S., Oshmyansky,A. and Yarus,M. (2005) Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids. Nucleic Acids Res., 33, 5924-5935.
47. Sabeti,P.C., Unrau,P.J. and Bartel,D.P. (1997) Accessing rare activities from random RNA sequences: The importance of the length of molecules in the starting pool. Chem. Biol., 4, 767-774.
48. Carothers,J.M., Oestreich,S.C., Davis,J.H. and Szostak,J.W. (2004) Informational complexity and functional activity of RNA structures. J. Am. Chem. Soc., 126, 5130-5137.
49. Legiewicz,M., Lozupone,C., Knight,R. and Yarus,M. (2005) Size, constant sequences, and optimal selection. RNA, 11, 1701-1709.