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Volumn 43, Issue 30, 2004, Pages 9695-9707

Tracing sequence diversity change of RNA-cleaving deoxyribozymes under increasing selection pressure during in vitro selection

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CHEMICAL REACTIONS; DNA; ENZYMES; PRESSURE EFFECTS; RNA;

EID: 3342955521     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049757j     Document Type: Article
Times cited : (53)

References (58)
  • 1
    • 0034671699 scopus 로고    scopus 로고
    • Making catalytic DNAs
    • Breaker, R. R. (2000) Making catalytic DNAs, Science 290, 2095-2096.
    • (2000) Science , vol.290 , pp. 2095-2096
    • Breaker, R.R.1
  • 3
    • 0031151976 scopus 로고    scopus 로고
    • DNA aptamers and DNA enzymes
    • Breaker, R. R. (1997) DNA aptamers and DNA enzymes, Curr. Opin. Chem. Biol. 1, 26-31.
    • (1997) Curr. Opin. Chem. Biol. , vol.1 , pp. 26-31
    • Breaker, R.R.1
  • 4
    • 0036240768 scopus 로고    scopus 로고
    • Deoxyribozymes: New activities and new applications
    • Emilsson, G. M., and Breaker, R. R. (2002) Deoxyribozymes: new activities and new applications, Cell. Mol. Life Sci. 59, 596-607.
    • (2002) Cell. Mol. Life Sci. , vol.59 , pp. 596-607
    • Emilsson, G.M.1    Breaker, R.R.2
  • 5
    • 0033150946 scopus 로고    scopus 로고
    • Deoxyribozymes: New players in the ancient game of biocatalysis
    • Li, Y., and Breaker, R. R. (1999) Deoxyribozymes: new players in the ancient game of biocatalysis, Curr. Opin. Struct. Biol. 9, 315-323.
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 315-323
    • Li, Y.1    Breaker, R.R.2
  • 7
    • 0028675028 scopus 로고
    • A DNA enzyme that cleaves RNA
    • Breaker, R. R., and Joyce, G. F. (1994) A DNA enzyme that cleaves RNA, Chem. Biol. 1, 223-229.
    • (1994) Chem. Biol. , vol.1 , pp. 223-229
    • Breaker, R.R.1    Joyce, G.F.2
  • 8
    • 0028983570 scopus 로고
    • A DNA enzyme with Mg(II)-dependent RNA phosphoesterase activity
    • Breaker, R. R., and Joyce, G. F. (1995) A DNA enzyme with Mg(II)-dependent RNA phosphoesterase activity. Chem. Biol. 2. 655-660.
    • (1995) Chem. Biol. , vol.2 , pp. 655-660
    • Breaker, R.R.1    Joyce, G.F.2
  • 9
    • 3342900163 scopus 로고    scopus 로고
    • The Ca(II) ion as a cofactor for a novel RNA-cleaving deoxyribozyme
    • Faulhammer, D., and Famulok, M. (1996) The Ca(II) ion as a cofactor for a novel RNA-cleaving deoxyribozyme, Angew. Chem., Int. Ed. Engl. 35, 2809-2813.
    • (1996) Angew. Chem., Int. Ed. Engl. , vol.35 , pp. 2809-2813
    • Faulhammer, D.1    Famulok, M.2
  • 10
  • 11
    • 0031215119 scopus 로고    scopus 로고
    • Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme
    • Geyer, C. R., and Sen, D. (1997) Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme, Chem. Biol. 4, 579-593.
    • (1997) Chem. Biol. , vol.4 , pp. 579-593
    • Geyer, C.R.1    Sen, D.2
  • 12
    • 0032568656 scopus 로고    scopus 로고
    • An amino acid as a cofactor for a catalytic polynucleotide
    • Roth, A., and Breaker, R. R. (1998) An amino acid as a cofactor for a catalytic polynucleotide, Proc. Natl. Acad. Sci. U.S.A. 95, 6027-6031.
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 6027-6031
    • Roth, A.1    Breaker, R.R.2
  • 14
    • 0034650291 scopus 로고    scopus 로고
    • In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme
    • 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.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 481-488
    • Li, J.1    Zheng, W.2    Kwon, A.H.3    Lu, Y.4
  • 15
    • 0035914482 scopus 로고    scopus 로고
    • A new and efficient DNA enzyme for the sequence-specific cleavage of RNA
    • 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.
    • (2001) J. Mol. Biol. , vol.313 , pp. 283-294
    • Feldman, A.R.1    Sen, D.2
  • 16
    • 0035961485 scopus 로고    scopus 로고
    • Bridging the gap between proteins and nucleic acids: A metal-independent RNAseA mimic with two protein-like functionalities
    • Perrin, D. M., Garestier, T., and Helene, C. (2001) Bridging the gap between proteins and nucleic acids: a metal-independent RNAseA mimic with two protein-like functionalities, J. Am. Chem. Soc. 123, 1556-1563.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 1556-1563
    • Perrin, D.M.1    Garestier, T.2    Helene, C.3
  • 17
    • 0037870470 scopus 로고    scopus 로고
    • Assemblage of signaling DNA enzymes with intriguing metal-ion specificities and pH dependences
    • Liu, Z., Mei, S. H., Brennan, J. D., and Li, Y. (2003) Assemblage of signaling DNA enzymes with intriguing metal-ion specificities and pH dependences, J. Am. Chem. Soc. 125, 7539-7545.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 7539-7545
    • Liu, Z.1    Mei, S.H.2    Brennan, J.D.3    Li, Y.4
  • 18
    • 0037438394 scopus 로고    scopus 로고
    • An efficient RNA-cleaving DNA enzyme that synchronizes catalysis with fluorescence signaling
    • Mei, S. H., Liu, Z., Brennan, J. D., and Li, Y. (2003) An efficient RNA-cleaving DNA enzyme that synchronizes catalysis with fluorescence signaling, J. Am. Chem. Soc. 125, 412-420.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 412-420
    • Mei, S.H.1    Liu, Z.2    Brennan, J.D.3    Li, Y.4
  • 19
    • 1142281951 scopus 로고    scopus 로고
    • Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme
    • Cruz. R. P. G., Withers, J. W., and Li. Y. (2004) Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme, Chem. Biol. 11, 57-67.
    • (2004) Chem. Biol. , vol.11 , pp. 57-67
    • Cruz, R.P.G.1    Withers, J.W.2    Li, Y.3
  • 20
    • 0037617490 scopus 로고    scopus 로고
    • In vitro evolution of an RNA-cleaving DNA enzyme into an RNA ligase switches the selectivity from 3′-5′ to 2′-5′
    • 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.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 5346-5350
    • Flynn-Charlebois, A.1    Prior, T.K.2    Hoadley, K.A.3    Silverman, S.K.4
  • 22
    • 0037675825 scopus 로고    scopus 로고
    • Optimization and generality of a small deoxyribozyme that ligates RNA
    • Ricca, B. L., Wolf, A. C., and Silverman, S. K. (2003) Optimization and generality of a small deoxyribozyme that ligates RNA, J. Mol. Biol. 330, 1015-1025.
    • (2003) J. Mol. Biol. , vol.330 , pp. 1015-1025
    • Ricca, B.L.1    Wolf, A.C.2    Silverman, S.K.3
  • 23
    • 0038210243 scopus 로고    scopus 로고
    • Deoxyribozymes that synthesize branched and lariat RNA
    • Wang, Y., and Silverman, S. K. (2003) Deoxyribozymes that synthesize branched and lariat RNA, J. Am. Chem. Soc. 125, 6880-6881.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 6880-6881
    • Wang, Y.1    Silverman, S.K.2
  • 25
    • 0030482173 scopus 로고    scopus 로고
    • In vitro selection of self-cleaving DNAs
    • Carmi, N., Shultz, L. A., and Breaker, R. R. (1996) In vitro selection of self-cleaving DNAs, Chem. Biol. 3, 1039-1046.
    • (1996) Chem. Biol. , vol.3 , pp. 1039-1046
    • Carmi, N.1    Shultz, L.A.2    Breaker, R.R.3
  • 26
    • 0029037713 scopus 로고
    • A DNA metalloenzyme with DNA ligase activity
    • Cuenoud, B., and Szostak, J. W. (1995) A DNA metalloenzyme with DNA ligase activity, Nature 375, 611-614.
    • (1995) Nature , vol.375 , pp. 611-614
    • Cuenoud, B.1    Szostak, J.W.2
  • 27
    • 0036148792 scopus 로고    scopus 로고
    • In vitro selection of a deoxyribozyme that can utilize multiple substrates
    • Levy, M., and Ellington, A. D. (2002) In vitro selection of a deoxyribozyme that can utilize multiple substrates, J. Mol. Evol. 54, 180-190.
    • (2002) J. Mol. Evol. , vol.54 , pp. 180-190
    • Levy, M.1    Ellington, A.D.2
  • 28
    • 0034840733 scopus 로고    scopus 로고
    • Selection of deoxyribozyme ligases that catalyze the formation of an unnatural internucleotide linkage
    • Levy, M., and Ellington, A. D. (2001) Selection of deoxyribozyme ligases that catalyze the formation of an unnatural internucleotide linkage, Bioorg. Med. Chem. 9, 2581-2587.
    • (2001) Bioorg. Med. Chem. , vol.9 , pp. 2581-2587
    • Levy, M.1    Ellington, A.D.2
  • 31
    • 0036235747 scopus 로고    scopus 로고
    • Sequence diversity, metal specificity, and catalytic proficiency of metal-dependent phosphorylating DNA enzymes
    • Wang, W., Billen, L. P., and Li, Y. (2002) Sequence diversity, metal specificity, and catalytic proficiency of metal-dependent phosphorylating DNA enzymes, Chem. Biol. 9, 507-517.
    • (2002) Chem. Biol. , vol.9 , pp. 507-517
    • Wang, W.1    Billen, L.P.2    Li, Y.3
  • 32
    • 0034696594 scopus 로고    scopus 로고
    • Capping DNA with DNA
    • Li, Y., Liu, Y., and Breaker, R. R. (2000) Capping DNA with DNA, Biochemistry 39, 3106-3114.
    • (2000) Biochemistry , vol.39 , pp. 3106-3114
    • Li, Y.1    Liu, Y.2    Breaker, R.R.3
  • 33
    • 0029945146 scopus 로고    scopus 로고
    • Recognition of anionic porphyrins by DNA aptamers
    • Li, Y., Geyer, C. R., and Sen, D. (1996) Recognition of anionic porphyrins by DNA aptamers, Biochemistry 35, 6911-6922.
    • (1996) Biochemistry , vol.35 , pp. 6911-6922
    • Li, Y.1    Geyer, C.R.2    Sen, D.3
  • 34
    • 0029746712 scopus 로고    scopus 로고
    • A catalytic DNA for porphyrin metalation
    • Li, Y., and Sen, D. (1996) A catalytic DNA for porphyrin metalation, Nat. Struct. Biol. 3, 743-747.
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 743-747
    • Li, Y.1    Sen, D.2
  • 35
    • 0030954291 scopus 로고    scopus 로고
    • Toward an efficient DNAzyme
    • Li, Y., and Sen, D. (1997) Toward an efficient DNAzyme, Biochemistry 36, 5589-5599.
    • (1997) Biochemistry , vol.36 , pp. 5589-5599
    • Li, Y.1    Sen, D.2
  • 36
    • 0031931019 scopus 로고    scopus 로고
    • The modus operandi of a DNA enzyme: Enhancement of substrate basicity
    • Li, Y., and Sen, D. (1998) The modus operandi of a DNA enzyme: enhancement of substrate basicity, Chem. Biol. 5, 1-12.
    • (1998) Chem. Biol. , vol.5 , pp. 1-12
    • Li, Y.1    Sen, D.2
  • 38
    • 0034254511 scopus 로고    scopus 로고
    • Molecular recognition of cAMP by an RNA aptamer
    • Koizumi, M., and Breaker, R. R. (2000) Molecular recognition of cAMP by an RNA aptamer, Biochemistry 39, 8983-8992.
    • (2000) Biochemistry , vol.39 , pp. 8983-8992
    • Koizumi, M.1    Breaker, R.R.2
  • 39
    • 0032558463 scopus 로고    scopus 로고
    • Mechanism and utility of an RNA-cleaving DNA enzyme
    • Santoro, S. W., and Joyce, G. F. (1998) Mechanism and utility of an RNA-cleaving DNA enzyme, Biochemistry 37, 13330-13342.
    • (1998) Biochemistry , vol.37 , pp. 13330-13342
    • Santoro, S.W.1    Joyce, G.F.2
  • 40
    • 0036001055 scopus 로고    scopus 로고
    • Catalytic DNA: A novel tool for gene suppression
    • Cairns, M. J., Saravolac, E. G., and Sun, L. Q. (2002) Catalytic DNA: a novel tool for gene suppression, Curr. Drug Targets 3, 269-279.
    • (2002) Curr. Drug Targets , vol.3 , pp. 269-279
    • Cairns, M.J.1    Saravolac, E.G.2    Sun, L.Q.3
  • 41
    • 0033709117 scopus 로고    scopus 로고
    • Catalytic DNAs as potential therapeutic agents and sequence-specific molecular tools to dissect biological function
    • Khachigian, L. M. (2000) Catalytic DNAs as potential therapeutic agents and sequence-specific molecular tools to dissect biological function, J. Clin. Invest. 106, 1189-1195.
    • (2000) J. Clin. Invest. , vol.106 , pp. 1189-1195
    • Khachigian, L.M.1
  • 42
    • 0037192355 scopus 로고    scopus 로고
    • Coating stents with antirestenotic drugs: The blunderbuss or the magic bullet?
    • Lowe, H. C., and Khachigian, L. M. (2002) Coating stents with antirestenotic drugs: the blunderbuss or the magic bullet?, Circulation 105, E29.
    • (2002) Circulation , vol.105
    • Lowe, H.C.1    Khachigian, L.M.2
  • 43
    • 0034715471 scopus 로고    scopus 로고
    • A highly sensitive and selective catalytic DNA biosensor for lead Ions
    • Li, J., and Lu, Y. (2000) A highly sensitive and selective catalytic DNA biosensor for lead Ions, J. Am. Chem. Soc. 122, 10466-10467.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 10466-10467
    • Li, J.1    Lu, Y.2
  • 46
    • 0042360338 scopus 로고    scopus 로고
    • A deoxyribozyme-based molecular automaton
    • Stojanovic, M. N., and Stefanovic, D. (2003) A deoxyribozyme-based molecular automaton, Nat. Biotechnol. 21, 1069-1074.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 1069-1074
    • Stojanovic, M.N.1    Stefanovic, D.2
  • 48
    • 0035851218 scopus 로고    scopus 로고
    • Catalytic oligodeoxynucleotides define a key regulatory role for early growth response factor-1 in the porcine model of coronary instent restenosis
    • Lowe, H. C., Fahmy, R. G., Kavurma, M. M., Baker, A., Chesterman, C. N., and Khachigian, L. M. (2001) Catalytic oligodeoxynucleotides define a key regulatory role for early growth response factor-1 in the porcine model of coronary instent restenosis, Circ. Res. 89, 670-677.
    • (2001) Circ. Res. , vol.89 , pp. 670-677
    • Lowe, H.C.1    Fahmy, R.G.2    Kavurma, M.M.3    Baker, A.4    Chesterman, C.N.5    Khachigian, L.M.6
  • 49
    • 0035662558 scopus 로고    scopus 로고
    • Nucleic acid based strategies as potential therapeutic tools: Mechanistic considerations and implications to restenosis
    • Santiago, F. S., and Khachigian, L. M. (2001) Nucleic acid based strategies as potential therapeutic tools: mechanistic considerations and implications to restenosis, J. Mol. Med. 79, 695-706.
    • (2001) J. Mol. Med. , vol.79 , pp. 695-706
    • Santiago, F.S.1    Khachigian, L.M.2
  • 50
    • 0034255112 scopus 로고    scopus 로고
    • Homogeneous assays based on deoxyribozyme catalysis
    • Stojanovic, M. N., de Prada, P., and Landry, D. W. (2000) Homogeneous assays based on deoxyribozyme catalysis, Nucleic Acids Res. 28, 2915-2918.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 2915-2918
    • Stojanovic, M.N.1    De Prada, P.2    Landry, D.W.3
  • 51
    • 0031259915 scopus 로고    scopus 로고
    • Accessing rare activities from random RNA sequences: The importance of the length of molecules in the starting pool
    • 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.
    • (1997) Chem. Biol. , vol.4 , pp. 767-774
    • Sabeti, P.C.1    Unrau, P.J.2    Bartel, D.P.3
  • 52
    • 0033575087 scopus 로고    scopus 로고
    • Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2′-hydroxyl group
    • Li, Y., and Breaker, R. R. (1999) Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2′-hydroxyl group, J. Am. Chem. Soc. 121, 5364-5372.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 5364-5372
    • Li, Y.1    Breaker, R.R.2
  • 53
    • 0014422451 scopus 로고
    • Interaction of metal ions with polynucleotides and related compounds. XII. The relative effect of various metal ions on DNA helicity
    • Eichhorn, G. L., and Shin, Y. A. (1968) Interaction of metal ions with polynucleotides and related compounds. XII. The relative effect of various metal ions on DNA helicity, J. Am. Chem. Soc. 90, 7323-7328.
    • (1968) J. Am. Chem. Soc. , vol.90 , pp. 7323-7328
    • Eichhorn, G.L.1    Shin, Y.A.2
  • 54
    • 0017147346 scopus 로고
    • Cooperative disordering of single-stranded polynucleotides through copper cross-linking
    • Rifkind, J. M., Shin, Y. A., Heim, J. M., and Eichhorn, G. L. (1976) Cooperative disordering of single-stranded polynucleotides through copper cross-linking, Biopolymers 15, 1879-1902.
    • (1976) Biopolymers , vol.15 , pp. 1879-1902
    • Rifkind, J.M.1    Shin, Y.A.2    Heim, J.M.3    Eichhorn, G.L.4
  • 55
    • 0034847558 scopus 로고    scopus 로고
    • Characterization of a DNA-cleaving deoxyribozyme
    • Carmi, N., and Breaker, R. R. (2001) Characterization of a DNA-cleaving deoxyribozyme, Bioorg. Med. Chem. 9, 2589-2600.
    • (2001) Bioorg. Med. Chem. , vol.9 , pp. 2589-2600
    • Carmi, N.1    Breaker, R.R.2
  • 56
    • 0026649231 scopus 로고
    • Directed evolution of an RNA enzyme
    • Beaudry, A. A., and Joyce, G. F. (1992) Directed evolution of an RNA enzyme, Science 257, 635-641.
    • (1992) Science , vol.257 , pp. 635-641
    • Beaudry, A.A.1    Joyce, G.F.2
  • 57
    • 1142277795 scopus 로고    scopus 로고
    • Assessing the likelihood of recurrence during RNA evolution in vitro
    • Lehman, N. (2004) Assessing the likelihood of recurrence during RNA evolution in vitro, Artif. Life 10, 1-22.
    • (2004) Artif. Life , vol.10 , pp. 1-22
    • Lehman, N.1
  • 58
    • 0027488624 scopus 로고
    • Isolation of new ribozymes from a large pool of random sequences
    • Bartel, D. P., and Szostak, J. W. (1993) Isolation of new ribozymes from a large pool of random sequences, Science 261, 1411-1418.
    • (1993) Science , vol.261 , pp. 1411-1418
    • Bartel, D.P.1    Szostak, J.W.2


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