메뉴 건너뛰기




Volumn 106, Issue , 2016, Pages 66-75

In vitro selection of RNA-cleaving DNAzymes for bacterial detection

Author keywords

Bacterial detection; Biosensor; Clostridium difficile; DNAzyme; In vitro selection; RNA cleavage

Indexed keywords

DEOXYRIBOZYME; RNA; SINGLE STRANDED DNA;

EID: 84961990920     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2016.03.018     Document Type: Article
Times cited : (45)

References (101)
  • 1
    • 0023364038 scopus 로고
    • The chemistry of self-splicing RNA and RNA enzymes
    • Cech, T.R., The chemistry of self-splicing RNA and RNA enzymes. Science 236 (1987), 1532–1539.
    • (1987) Science , vol.236 , pp. 1532-1539
    • Cech, T.R.1
  • 2
    • 0034603154 scopus 로고    scopus 로고
    • Adaptive recognition by nucleic acid aptamers
    • Hermann, T., Patel, D.J., Adaptive recognition by nucleic acid aptamers. Science 287 (2000), 820–825.
    • (2000) Science , vol.287 , pp. 820-825
    • Hermann, T.1    Patel, D.J.2
  • 4
    • 67650713931 scopus 로고    scopus 로고
    • The structural and functional diversity of metabolite-binding riboswitches
    • Roth, A., Breaker, R.R., The structural and functional diversity of metabolite-binding riboswitches. Annu. Rev. Biochem. 78 (2009), 305–334.
    • (2009) Annu. Rev. Biochem. , vol.78 , pp. 305-334
    • Roth, A.1    Breaker, R.R.2
  • 5
    • 77957743184 scopus 로고    scopus 로고
    • Evolution of biological catalysis: ribozyme to RNP enzyme
    • Cech, T.R., Evolution of biological catalysis: ribozyme to RNP enzyme. Cold Spring Harbor Symp. Quant. Biol. 74 (2009), 11–16.
    • (2009) Cold Spring Harbor Symp. Quant. Biol. , vol.74 , pp. 11-16
    • Cech, T.R.1
  • 6
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific ligands
    • Ellington, A.D., Szostak, J.W., In vitro selection of RNA molecules that bind specific ligands. Nature 346 (1990), 818–822.
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 7
    • 0025194307 scopus 로고
    • Systematic evolution of ligand by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • Tuerk, C., Gold, L., Systematic evolution of ligand by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249 (1990), 505–510.
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 8
    • 0025332385 scopus 로고
    • Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA
    • Robertson, D.L., Joyce, G.F., Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344 (1990), 467–468.
    • (1990) Nature , vol.344 , pp. 467-468
    • Robertson, D.L.1    Joyce, G.F.2
  • 9
    • 0032853242 scopus 로고    scopus 로고
    • In vitro selection of functional nucleic acids
    • Wilson, D.S., Szostak, J.W., In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68 (1999), 611–647.
    • (1999) Annu. Rev. Biochem. , vol.68 , pp. 611-647
    • Wilson, D.S.1    Szostak, J.W.2
  • 10
    • 0028675028 scopus 로고
    • A DNA enzyme that cleaves RNA
    • Breaker, R.R., Joyce, G.F., A DNA enzyme that cleaves RNA. Chem. Biol. 1 (1994), 223–229.
    • (1994) Chem. Biol. , vol.1 , pp. 223-229
    • Breaker, R.R.1    Joyce, G.F.2
  • 11
    • 0029037713 scopus 로고
    • A DNA metalloenzyme with DNA ligase activity
    • Cuenoud, B., Szostak, J.W., A DNA metalloenzyme with DNA ligase activity. Nature 375 (1995), 611–614.
    • (1995) Nature , vol.375 , pp. 611-614
    • Cuenoud, B.1    Szostak, J.W.2
  • 12
    • 0026575221 scopus 로고
    • Selection of single-stranded DNA molecules that bind and inhibit human thrombin
    • Bock, L.C., Griffin, L.C., Latham, J.A., Vermaas, E.H., Toole, J.J., Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 355 (1992), 564–566.
    • (1992) Nature , vol.355 , pp. 564-566
    • Bock, L.C.1    Griffin, L.C.2    Latham, J.A.3    Vermaas, E.H.4    Toole, J.J.5
  • 13
    • 0026599465 scopus 로고
    • Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures
    • Ellington, A.D., Szostak, J.W., Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures. Nature 355 (1992), 850–852.
    • (1992) Nature , vol.355 , pp. 850-852
    • Ellington, A.D.1    Szostak, J.W.2
  • 14
    • 66249097058 scopus 로고    scopus 로고
    • Functional nucleic acid sensors
    • Liu, J., Cao, Z., Lu, Y., Functional nucleic acid sensors. Chem. Rev. 109 (2009), 1948–1998.
    • (2009) Chem. Rev. , vol.109 , pp. 1948-1998
    • Liu, J.1    Cao, Z.2    Lu, Y.3
  • 15
    • 62649161589 scopus 로고    scopus 로고
    • Biologically inspired synthetic enzymes made from DNA
    • Schlosser, K., Li, Y., Biologically inspired synthetic enzymes made from DNA. Chem. Biol. 16 (2009), 311–322.
    • (2009) Chem. Biol. , vol.16 , pp. 311-322
    • Schlosser, K.1    Li, Y.2
  • 16
    • 33744548059 scopus 로고    scopus 로고
    • Nucleic acid aptamers and enzymes as sensors
    • Navani, N.K., Li, Y., Nucleic acid aptamers and enzymes as sensors. Curr. Opin. Chem. Biol. 10 (2006), 272–281.
    • (2006) Curr. Opin. Chem. Biol. , vol.10 , pp. 272-281
    • Navani, N.K.1    Li, Y.2
  • 18
    • 0036235747 scopus 로고    scopus 로고
    • Sequence diversity, metal specificity, and catalytic proficiency of metal-dependent phosphorylating DNA enzymes
    • Wang, W., Billen, L.P., Li, Y., Sequence diversity, metal specificity, and catalytic proficiency of metal-dependent phosphorylating DNA enzymes. Chem. Biol. 9 (2002), 507–517.
    • (2002) Chem. Biol. , vol.9 , pp. 507-517
    • Wang, W.1    Billen, L.P.2    Li, Y.3
  • 19
    • 0034696594 scopus 로고    scopus 로고
    • Capping DNA with DNA
    • Li, Y., Liu, Y., Breaker, R.R., Capping DNA with DNA. Biochemistry 39 (2000), 3106–3114.
    • (2000) Biochemistry , vol.39 , pp. 3106-3114
    • Li, Y.1    Liu, Y.2    Breaker, R.R.3
  • 23
    • 0347089036 scopus 로고    scopus 로고
    • A deoxyribozymes that harnesses light to repair thymine dimers in DNA
    • Chinnapen, D.J., Sen, D., A deoxyribozymes that harnesses light to repair thymine dimers in DNA. Proc. Natl. Acad. Sci. U.S.A. 101 (2004), 65–69.
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 65-69
    • Chinnapen, D.J.1    Sen, D.2
  • 24
    • 70349327390 scopus 로고    scopus 로고
    • DNA-catalyzed sequence-specific hydrolysis of DNA
    • Chandra, M., Sachdeva, A., Silverman, S.K., DNA-catalyzed sequence-specific hydrolysis of DNA. Nat. Chem. Biol. 5 (2009), 718–720.
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 718-720
    • Chandra, M.1    Sachdeva, A.2    Silverman, S.K.3
  • 26
    • 0023663396 scopus 로고
    • Self-cleavage of plus and minus RNA of a virusoid and a structural model for the active sites
    • Forster, A.C., Symons, R.H., Self-cleavage of plus and minus RNA of a virusoid and a structural model for the active sites. Cell 49 (1987), 211–220.
    • (1987) Cell , vol.49 , pp. 211-220
    • Forster, A.C.1    Symons, R.H.2
  • 27
    • 0024340908 scopus 로고
    • RNA catalytic properties of the minimum (-)sTRSV sequence
    • Hampel, A., Tritz, R., RNA catalytic properties of the minimum (-)sTRSV sequence. Biochemistry 28 (1989), 4929–4933.
    • (1989) Biochemistry , vol.28 , pp. 4929-4933
    • Hampel, A.1    Tritz, R.2
  • 28
    • 0024209351 scopus 로고
    • Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus
    • Kuo, M.Y., Sharmeen, L., Dinter-Gottlieb, G., Taylor, J., Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus. J. Virol. 62 (1988), 4439–4444.
    • (1988) J. Virol. , vol.62 , pp. 4439-4444
    • Kuo, M.Y.1    Sharmeen, L.2    Dinter-Gottlieb, G.3    Taylor, J.4
  • 29
    • 0025333084 scopus 로고
    • A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria
    • Saville, B.J., Collins, R.A., A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria. Cell 61 (1990), 685–696.
    • (1990) Cell , vol.61 , pp. 685-696
    • Saville, B.J.1    Collins, R.A.2
  • 30
    • 1642586299 scopus 로고    scopus 로고
    • Control of gene expression by a natural metabolite-responsive ribozyme
    • Winkler, W.C., Nahvi, A., Roth, A., Collins, J.A., Breaker, R.R., Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428 (2004), 281–286.
    • (2004) Nature , vol.428 , pp. 281-286
    • Winkler, W.C.1    Nahvi, A.2    Roth, A.3    Collins, J.A.4    Breaker, R.R.5
  • 31
    • 0028983570 scopus 로고
    • 2+-dependent RNA phosphoesterase activity
    • 2+-dependent RNA phosphoesterase activity. Chem. Biol. 2 (1995), 655–660.
    • (1995) Chem. Biol. , vol.2 , pp. 655-660
    • Breaker, R.R.1    Joyce, G.F.2
  • 32
    • 0030498356 scopus 로고    scopus 로고
    • 2+ ion as a cofactor for a novel RNA-cleaving deoxyribozymes
    • 2+ ion as a cofactor for a novel RNA-cleaving deoxyribozymes. Angew. Chem., Int. Ed. Engl. 35 (1996), 2837–2841.
    • (1996) Angew. Chem., Int. Ed. Engl. , vol.35 , pp. 2837-2841
    • Faulhammer, D.1    Famulok, M.2
  • 33
  • 34
    • 0031215119 scopus 로고    scopus 로고
    • Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme
    • Geyer, C.R., Sen, D., Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme. Chem. Biol. 4 (1997), 579–593.
    • (1997) Chem. Biol. , vol.4 , pp. 579-593
    • Geyer, C.R.1    Sen, D.2
  • 36
    • 0034650291 scopus 로고    scopus 로고
    • In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozymes
    • Li, J., Zheng, W., Kwon, A.H., Lu, Y., In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozymes. Nucleic Acids Res. 28 (2000), 481–488.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 481-488
    • Li, J.1    Zheng, W.2    Kwon, A.H.3    Lu, Y.4
  • 37
    • 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., Hélène, C., Bridging the gap between proteins and nucleic acids: a metal-independent RNaseA mimic with two protein like functionalities. J. Am. Chem. Soc. 123 (2001), 1556–1563.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 1556-1563
    • Perrin, D.M.1    Garestier, T.2    Hélène, C.3
  • 38
    • 0037438394 scopus 로고    scopus 로고
    • An efficient RNA-cleaving DNA enzyme that synchronizes catalysis with fluorescence signaling
    • Mei, S.H.J., Liu, Z., Brennan, J.D., Li, Y., An efficient RNA-cleaving DNA enzyme that synchronizes catalysis with fluorescence signaling. J. Am. Chem. Soc. 125 (2003), 412–420.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 412-420
    • Mei, S.H.J.1    Liu, Z.2    Brennan, J.D.3    Li, Y.4
  • 39
    • 0037870470 scopus 로고    scopus 로고
    • Assemblage of signaling DNA enzymes with intriguing metal specificity and pH dependence
    • Liu, Z., Mei, S.H.J., Brennan, J.D., Li, Y., Assemblage of signaling DNA enzymes with intriguing metal specificity and pH dependence. J. Am. Chem. Soc. 125 (2003), 7539–7545.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 7539-7545
    • Liu, Z.1    Mei, S.H.J.2    Brennan, J.D.3    Li, Y.4
  • 40
    • 1842618467 scopus 로고    scopus 로고
    • Sequence-specific cleavage of RNA in the absence of divalent metal ions by a DNAzyme incorporating imidazolyl and amino functionalities
    • Sidorov, A.V., Grasby, J.A., Williams, D.M., Sequence-specific cleavage of RNA in the absence of divalent metal ions by a DNAzyme incorporating imidazolyl and amino functionalities. Nucleic Acids Res. 32 (2004), 1591–1601.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1591-1601
    • Sidorov, A.V.1    Grasby, J.A.2    Williams, D.M.3
  • 41
    • 1142281951 scopus 로고    scopus 로고
    • Dinucleotide junction cleavage versatility of 8–17 deoxyribozymes
    • Cruz, R.P., Withers, J.B., Li, Y., Dinucleotide junction cleavage versatility of 8–17 deoxyribozymes. Chem. Biol. 11 (2004), 57–67.
    • (2004) Chem. Biol. , vol.11 , pp. 57-67
    • Cruz, R.P.1    Withers, J.B.2    Li, Y.3
  • 42
    • 3342955521 scopus 로고    scopus 로고
    • Tracing sequence diversity change of RNA-cleaving deoxyribozymes under increasing selection pressure during in vitro selection
    • Schlosser, K., Li, Y., Tracing sequence diversity change of RNA-cleaving deoxyribozymes under increasing selection pressure during in vitro selection. Biochemistry 43 (2004), 9695–9707.
    • (2004) Biochemistry , vol.43 , pp. 9695-9707
    • Schlosser, K.1    Li, Y.2
  • 44
    • 24744435998 scopus 로고    scopus 로고
    • Diverse evolutionary trajectories characterize a community of RNA-cleaving deoxyribozymes: a case study into the population dynamics of in vitro selection
    • Schlosser, K., Li, Y., 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 (2005), 92–206.
    • (2005) J. Mol. Evol. , vol.61 , pp. 92-206
    • Schlosser, K.1    Li, Y.2
  • 45
    • 33646823318 scopus 로고    scopus 로고
    • Characterization of long RNA-cleaving deoxyribozymes with short catalytic cores: the effect of excess sequence elements on the outcome of in vitro selection
    • Schlosser, K., Lam, J.C., Li, Y., 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 (2006), 2445–2454.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 2445-2454
    • Schlosser, K.1    Lam, J.C.2    Li, Y.3
  • 46
    • 33847779647 scopus 로고    scopus 로고
    • A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity
    • Liu, J., Brown, A.K., Meng, X., Cropek, D.M., Istok, J.D., Watson, D.B., Lu, Y., A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity. Proc. Natl. Acad. Sci. U.S.A. 104 (2007), 2056–2061.
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 2056-2061
    • Liu, J.1    Brown, A.K.2    Meng, X.3    Cropek, D.M.4    Istok, J.D.5    Watson, D.B.6    Lu, Y.7
  • 47
    • 49249091384 scopus 로고    scopus 로고
    • In vitro selection of small RNA-cleaving deoxyribozymes that cleave pyrimidine-pyrimidine junctions
    • Schlosser, K., Gu, J., Lan, J.C.F., Li, Y., In vitro selection of small RNA-cleaving deoxyribozymes that cleave pyrimidine-pyrimidine junctions. Nucleic Acids Res. 36 (2008), 4768–4777.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 4768-4777
    • Schlosser, K.1    Gu, J.2    Lan, J.C.F.3    Li, Y.4
  • 48
    • 59649104166 scopus 로고    scopus 로고
    • DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides
    • Schlosser, K., Li, Y., DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides. Nucleic Acids Res. 37 (2009), 413–420.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 413-420
    • Schlosser, K.1    Li, Y.2
  • 49
    • 67649842764 scopus 로고    scopus 로고
    • A genotype-to-phenotype map of in vitro selected RNA-cleaving DNAzymes: implications for accessing the target phenotype
    • Schlosser, K., Lam, J.C., Li, Y., A genotype-to-phenotype map of in vitro selected RNA-cleaving DNAzymes: implications for accessing the target phenotype. Nucleic Acids Res. 37 (2009), 3545–3557.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 3545-3557
    • Schlosser, K.1    Lam, J.C.2    Li, Y.3
  • 50
    • 77954387386 scopus 로고    scopus 로고
    • A complex RNA-cleaving DNAzyme that can efficiently cleave a pyrimidine-pyrimidine junction
    • Lam, J.C., Withers, J.B., Li, Y., A complex RNA-cleaving DNAzyme that can efficiently cleave a pyrimidine-pyrimidine junction. J. Mol. Biol. 400 (2010), 689–701.
    • (2010) J. Mol. Biol. , vol.400 , pp. 689-701
    • Lam, J.C.1    Withers, J.B.2    Li, Y.3
  • 51
    • 79959284618 scopus 로고    scopus 로고
    • Characterization of non-8-17 sequences uncovers structurally diverse RNA-cleaving deoxyribozymes
    • Lam, J.C., Kwan, S.O., Li, Y., Characterization of non-8-17 sequences uncovers structurally diverse RNA-cleaving deoxyribozymes. Mol. Biosyst. 7 (2011), 2139–2146.
    • (2011) Mol. Biosyst. , vol.7 , pp. 2139-2146
    • Lam, J.C.1    Kwan, S.O.2    Li, Y.3
  • 52
    • 84907894839 scopus 로고    scopus 로고
    • In vitro selection of a new lanthanide-dependent DNAzyme for ratiometric sensing lanthanides
    • Huang, P.J., Vazin, M., Liu, J., In vitro selection of a new lanthanide-dependent DNAzyme for ratiometric sensing lanthanides. Anal. Chem. 86 (2014), 9993–9999.
    • (2014) Anal. Chem. , vol.86 , pp. 9993-9999
    • Huang, P.J.1    Vazin, M.2    Liu, J.3
  • 53
    • 84948388138 scopus 로고    scopus 로고
    • Searching for a DNAzyme version of the leadzyme
    • Saran, R., Chen, Q., Liu, J., Searching for a DNAzyme version of the leadzyme. J. Mol. Evol. 81 (2015), 235–244.
    • (2015) J. Mol. Evol. , vol.81 , pp. 235-244
    • Saran, R.1    Chen, Q.2    Liu, J.3
  • 56
    • 84948382395 scopus 로고    scopus 로고
    • +-specific DNAzyme motif from two in vitro selections under different conditions
    • +-specific DNAzyme motif from two in vitro selections under different conditions. J. Mol. Evol. 81 (2015), 225–234.
    • (2015) J. Mol. Evol. , vol.81 , pp. 225-234
    • Torabi, S.F.1    Lu, Y.2
  • 57
    • 84934903518 scopus 로고    scopus 로고
    • Evolution of an enzyme from a noncatalytic nucleic acid sequence
    • Gysbers, R., Tram, K., Gu, J., Li, Y., Evolution of an enzyme from a noncatalytic nucleic acid sequence. Sci. Rep., 5, 2015, 11405.
    • (2015) Sci. Rep. , vol.5 , pp. 11405
    • Gysbers, R.1    Tram, K.2    Gu, J.3    Li, Y.4
  • 58
    • 84929120225 scopus 로고    scopus 로고
    • An efficient catalytic DNA that cleaves L-RNA
    • Tram, K., Xia, J., Gysbers, R., Li, Y., An efficient catalytic DNA that cleaves L-RNA. PLoS One, 10, 2015, e0126402.
    • (2015) PLoS One , vol.10
    • Tram, K.1    Xia, J.2    Gysbers, R.3    Li, Y.4
  • 59
    • 84948387111 scopus 로고    scopus 로고
    • Sequence mutation and structural alteration transform a noncatalytic DNA sequence into an efficient RNA-cleaving DNAzyme
    • Chan, L., Tram, K., Gysbers, R., Gu, J., Li, Y., Sequence mutation and structural alteration transform a noncatalytic DNA sequence into an efficient RNA-cleaving DNAzyme. J. Mol. Evol. 81 (2015), 245–253.
    • (2015) J. Mol. Evol. , vol.81 , pp. 245-253
    • Chan, L.1    Tram, K.2    Gysbers, R.3    Gu, J.4    Li, Y.5
  • 60
    • 28544448500 scopus 로고    scopus 로고
    • In vitro selection, characterization, and application of deoxyribozymes that cleave RNA
    • Silverman, S.K., In vitro selection, characterization, and application of deoxyribozymes that cleave RNA. Nucleic Acids Res. 33 (2005), 6151–6163.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 6151-6163
    • Silverman, S.K.1
  • 61
    • 77951713609 scopus 로고    scopus 로고
    • A versatile endoribonuclease mimic made of DNA: characteristics and applications of the 8–17 RNA-cleaving DNAzyme
    • Schlosser, K., Li, Y., A versatile endoribonuclease mimic made of DNA: characteristics and applications of the 8–17 RNA-cleaving DNAzyme. ChemBioChem 11 (2010), 866–879.
    • (2010) ChemBioChem , vol.11 , pp. 866-879
    • Schlosser, K.1    Li, Y.2
  • 62
    • 0034715471 scopus 로고    scopus 로고
    • A highly sensitive and selective catalytic DNA biosensor for lead ions
    • Li, J., Lu, Y., A highly sensitive and selective catalytic DNA biosensor for lead ions. J. Am. Chem. Soc. 122 (2000), 10466–10467.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 10466-10467
    • Li, J.1    Lu, Y.2
  • 63
    • 0034255112 scopus 로고    scopus 로고
    • Homogeneous assays based on deoxyribozyme catalysis
    • Stojanovic, M.N., de Prada, P., Landry, D.W., Homogeneous assays based on deoxyribozyme catalysis. Nucleic Acids Res. 28 (2000), 2915–2918.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 2915-2918
    • Stojanovic, M.N.1    de Prada, P.2    Landry, D.W.3
  • 64
    • 0036301260 scopus 로고    scopus 로고
    • A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes
    • Wang, D.Y., Lai, B.H.Y., Sen, D., A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes. J. Mol. Biol. 318 (2002), 33–43.
    • (2002) J. Mol. Biol. , vol.318 , pp. 33-43
    • Wang, D.Y.1    Lai, B.H.Y.2    Sen, D.3
  • 65
    • 0038209225 scopus 로고    scopus 로고
    • A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles
    • Liu, J., Lu, Y., A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles. J. Am. Chem. Soc. 125 (2003), 6642–6643.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 6642-6643
    • Liu, J.1    Lu, Y.2
  • 67
    • 15744372570 scopus 로고    scopus 로고
    • Structure-switching allosteric deoxyribozymes
    • Achenbach, J.C., Nutiu, R., Li, Y., Structure-switching allosteric deoxyribozymes. Anal. Chim. Acta 534 (2005), 41–51.
    • (2005) Anal. Chim. Acta , vol.534 , pp. 41-51
    • Achenbach, J.C.1    Nutiu, R.2    Li, Y.3
  • 68
    • 33748570785 scopus 로고    scopus 로고
    • Catalytic and signaling properties of trans-acting pH6DZ1, an RNA-cleaving and fluorescence-signaling deoxyribozymes with a four-way junction structure
    • Shen, Y., Chiuman, W., Brennan, J.D., Li, Y., Catalytic and signaling properties of trans-acting pH6DZ1, an RNA-cleaving and fluorescence-signaling deoxyribozymes with a four-way junction structure. ChemBioChem 7 (2006), 1343–1348.
    • (2006) ChemBioChem , vol.7 , pp. 1343-1348
    • Shen, Y.1    Chiuman, W.2    Brennan, J.D.3    Li, Y.4
  • 69
    • 43249088030 scopus 로고    scopus 로고
    • Simple fluorescent sensors engineered with catalytic DNA ’MgZ’ based on a non-classic allosteric design
    • Chiuman, W., Li, Y., Simple fluorescent sensors engineered with catalytic DNA ’MgZ’ based on a non-classic allosteric design. PLoS One, 2, 2007, e1224.
    • (2007) PLoS One , vol.2
    • Chiuman, W.1    Li, Y.2
  • 70
    • 70350316755 scopus 로고    scopus 로고
    • Abasic site-containing DNAzyme and aptamer for label-free fluorescent detection of Pb(2+) and adenosine with high sensitivity, selectivity, and tunable dynamic range
    • Xiang, Y., Tong, A., Lu, Y., Abasic site-containing DNAzyme and aptamer for label-free fluorescent detection of Pb(2+) and adenosine with high sensitivity, selectivity, and tunable dynamic range. J. Am. Chem. Soc. 131 (2009), 15352–15357.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 15352-15357
    • Xiang, Y.1    Tong, A.2    Lu, Y.3
  • 71
    • 77952784379 scopus 로고    scopus 로고
    • A highly selective lead sensor based on a classic lead DNAzyme
    • Lan, T., Furuya, K., Lu, Y., A highly selective lead sensor based on a classic lead DNAzyme. Chem. Chmmun. 46 (2010), 3896–3898.
    • (2010) Chem. Chmmun. , vol.46 , pp. 3896-3898
    • Lan, T.1    Furuya, K.2    Lu, Y.3
  • 72
    • 79953722536 scopus 로고    scopus 로고
    • Fluorogenic DNAzyme probes as bacterial indicators
    • Ali, M.M., Aguirre, S.D., Lazim, H., Li, Y., Fluorogenic DNAzyme probes as bacterial indicators. Angew. Chem., Int. Ed. 50 (2011), 3751–3754.
    • (2011) Angew. Chem., Int. Ed. , vol.50 , pp. 3751-3754
    • Ali, M.M.1    Aguirre, S.D.2    Lazim, H.3    Li, Y.4
  • 73
    • 80052129556 scopus 로고    scopus 로고
    • Using personal glucose meters and functional DNA sensors to quantify a variety of analytical targets
    • Xiang, Y., Lu, Y., Using personal glucose meters and functional DNA sensors to quantify a variety of analytical targets. Nat. Chem. 3 (2011), 697–703.
    • (2011) Nat. Chem. , vol.3 , pp. 697-703
    • Xiang, Y.1    Lu, Y.2
  • 74
    • 84863362127 scopus 로고    scopus 로고
    • Label-free catalytic and molecular beacon containing an abasic site for sensitive fluorescent detection of small inorganic and organic molecules
    • Song, P., Xiang, Y., Xing, H., Zhou, Z., Tong, A., Lu, Y., Label-free catalytic and molecular beacon containing an abasic site for sensitive fluorescent detection of small inorganic and organic molecules. Anal. Chem. 84 (2012), 2916–2922.
    • (2012) Anal. Chem. , vol.84 , pp. 2916-2922
    • Song, P.1    Xiang, Y.2    Xing, H.3    Zhou, Z.4    Tong, A.5    Lu, Y.6
  • 75
    • 84876014910 scopus 로고    scopus 로고
    • A DNAzyme-gold nanoparticle probe for uranyl ion in living cells
    • Wu, P., Hwang, K., Lan, T., Lu, Y., A DNAzyme-gold nanoparticle probe for uranyl ion in living cells. J. Am. Chem. Soc. 135 (2013), 5254–5257.
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 5254-5257
    • Wu, P.1    Hwang, K.2    Lan, T.3    Lu, Y.4
  • 76
    • 84893540958 scopus 로고    scopus 로고
    • Ultrasensitive DNAzyme beacon for lanthanides and metal speciation
    • Huang, P.J., Lin, J., Cao, J., Vazin, M., Liu, J., Ultrasensitive DNAzyme beacon for lanthanides and metal speciation. Anal. Chem. 86 (2014), 1816–1821.
    • (2014) Anal. Chem. , vol.86 , pp. 1816-1821
    • Huang, P.J.1    Lin, J.2    Cao, J.3    Vazin, M.4    Liu, J.5
  • 77
    • 84945312310 scopus 로고    scopus 로고
    • Desulfurization activated phosphorothioate DNAzyme for the detection of thallium
    • Huang, P.J., Vazin, M., Liu, J., Desulfurization activated phosphorothioate DNAzyme for the detection of thallium. Anal. Chem. 87 (2015), 10443–10449.
    • (2015) Anal. Chem. , vol.87 , pp. 10443-10449
    • Huang, P.J.1    Vazin, M.2    Liu, J.3
  • 78
    • 84919360843 scopus 로고    scopus 로고
    • Photocaged DNAzymes as a general method for sensing metal ions in living cells
    • Hwang, K., Wu, P., Kim, T., Lei, L., Tian, S., Wang, Y., Lu, Y., Photocaged DNAzymes as a general method for sensing metal ions in living cells. Angew. Chem., Int. Ed. 53 (2014), 13798–13802.
    • (2014) Angew. Chem., Int. Ed. , vol.53 , pp. 13798-13802
    • Hwang, K.1    Wu, P.2    Kim, T.3    Lei, L.4    Tian, S.5    Wang, Y.6    Lu, Y.7
  • 79
    • 84902839075 scopus 로고    scopus 로고
    • Sensing parts-per-trillion Cd(2+), Hg(2+), and Pb(2+) collectively and individually using phosphorothioate DNAzymes
    • Huang, P.J., Liu, J., Sensing parts-per-trillion Cd(2+), Hg(2+), and Pb(2+) collectively and individually using phosphorothioate DNAzymes. Anal. Chem. 86 (2014), 5999–6005.
    • (2014) Anal. Chem. , vol.86 , pp. 5999-6005
    • Huang, P.J.1    Liu, J.2
  • 80
    • 84911370453 scopus 로고    scopus 로고
    • Translating bacterial detection by DNAzymes into a litmus test
    • Tram, K., Kanda, P., Salena, B.J., Huan, S., Li, Y., Translating bacterial detection by DNAzymes into a litmus test. Angew. Chem., Int. Ed. 53 (2014), 12799–12802.
    • (2014) Angew. Chem., Int. Ed. , vol.53 , pp. 12799-12802
    • Tram, K.1    Kanda, P.2    Salena, B.J.3    Huan, S.4    Li, Y.5
  • 81
    • 84920392829 scopus 로고    scopus 로고
    • Highly specific recognition of breast tumors by an RNA-cleaving fluorogenic DNAzyme probe
    • He, S., Qu, L., Shen, Z., Tan, Y., Zeng, M., Liu, F., Jiang, Y., Li, Y., Highly specific recognition of breast tumors by an RNA-cleaving fluorogenic DNAzyme probe. Anal. Chem. 87 (2015), 569–577.
    • (2015) Anal. Chem. , vol.87 , pp. 569-577
    • He, S.1    Qu, L.2    Shen, Z.3    Tan, Y.4    Zeng, M.5    Liu, F.6    Jiang, Y.7    Li, Y.8
  • 83
    • 24644519818 scopus 로고    scopus 로고
    • Characterizing the secondary structure and identifying functionally essential nucleotides of pH6DZ1, a fluorescence-signaling and RNA-cleaving deoxyribozymes
    • Shen, Y., Brennan, J.D., Li, Y., Characterizing the secondary structure and identifying functionally essential nucleotides of pH6DZ1, a fluorescence-signaling and RNA-cleaving deoxyribozymes. Biochemistry 44 (2005), 12066–12076.
    • (2005) Biochemistry , vol.44 , pp. 12066-12076
    • Shen, Y.1    Brennan, J.D.2    Li, Y.3
  • 84
    • 33749678681 scopus 로고    scopus 로고
    • Evolution of high-branching deoxyribozymes from a catalytic DNA with a three-way junction
    • Chiuman, W., Li, Y., Evolution of high-branching deoxyribozymes from a catalytic DNA with a three-way junction. Chem. Biol. 13 (2006), 1061–1069.
    • (2006) Chem. Biol. , vol.13 , pp. 1061-1069
    • Chiuman, W.1    Li, Y.2
  • 85
    • 33644962875 scopus 로고    scopus 로고
    • Revitalization of six abandoned catalytic DNA species reveals a common three-way junction framework and diverse catalytic cores
    • Chiuman, W., Li, Y., Revitalization of six abandoned catalytic DNA species reveals a common three-way junction framework and diverse catalytic cores. J. Mol. Biol. 357 (2006), 748–754.
    • (2006) J. Mol. Biol. , vol.357 , pp. 748-754
    • Chiuman, W.1    Li, Y.2
  • 86
    • 31144444656 scopus 로고    scopus 로고
    • Characterization of a catalytically efficient acidic RNA-cleaving deoxyribozymes
    • Kandadai, S.A., Li, Y., Characterization of a catalytically efficient acidic RNA-cleaving deoxyribozymes. Nucleic Acids Res. 33 (2006), 7164–7175.
    • (2006) Nucleic Acids Res. , vol.33 , pp. 7164-7175
    • Kandadai, S.A.1    Li, Y.2
  • 87
    • 31444452036 scopus 로고    scopus 로고
    • Quenching of fluorophore-labeled DNA oligonucleotides by divalent metal ions: implications for selection, design, and applications of signaling aptamers and signaling deoxyribozymes
    • Rupcich, N., Chiuman, W., Nutiu, R., Mei, S., Flora, K.K., Li, Y., Brennan, J.D., Quenching of fluorophore-labeled DNA oligonucleotides by divalent metal ions: implications for selection, design, and applications of signaling aptamers and signaling deoxyribozymes. J. Am. Chem. Soc. 128 (2006), 780–790.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 780-790
    • Rupcich, N.1    Chiuman, W.2    Nutiu, R.3    Mei, S.4    Flora, K.K.5    Li, Y.6    Brennan, J.D.7
  • 88
    • 33846913441 scopus 로고    scopus 로고
    • Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates
    • Chiuman, W., Li, Y., Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates. Nucleic Acids Res. 35 (2007), 401–405.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 401-405
    • Chiuman, W.1    Li, Y.2
  • 89
    • 68249102833 scopus 로고    scopus 로고
    • Characterization and optimization of an RNA-cleaving deoxyribozymes active at pH 5
    • Kandadai, S.A., Mok, W.W.K., Ali, M.M., Li, Y., Characterization and optimization of an RNA-cleaving deoxyribozymes active at pH 5. Biochemistry 48 (2009), 7383–7391.
    • (2009) Biochemistry , vol.48 , pp. 7383-7391
    • Kandadai, S.A.1    Mok, W.W.K.2    Ali, M.M.3    Li, Y.4
  • 90
    • 34248198976 scopus 로고    scopus 로고
    • Entrapment of fluorescence-signaling DNA enzymes in sol-gel derived materials for metal ion sensing
    • Shen, Y., Mackey, G., Rupcich, N., Gloster, D., Chiuman, W., Li, Y., Brennan, J.D., Entrapment of fluorescence-signaling DNA enzymes in sol-gel derived materials for metal ion sensing. Anal. Chem. 79 (2007), 3494–3503.
    • (2007) Anal. Chem. , vol.79 , pp. 3494-3503
    • Shen, Y.1    Mackey, G.2    Rupcich, N.3    Gloster, D.4    Chiuman, W.5    Li, Y.6    Brennan, J.D.7
  • 91
    • 84863251023 scopus 로고    scopus 로고
    • Developing fluorogenic RNA-cleaving DNAzymes for biosensing applications
    • Ali, M.M., Aguirre, S.D., Mok, W.W., Li, Y., Developing fluorogenic RNA-cleaving DNAzymes for biosensing applications. Methods Mol. Biol. 848 (2012), 395–418.
    • (2012) Methods Mol. Biol. , vol.848 , pp. 395-418
    • Ali, M.M.1    Aguirre, S.D.2    Mok, W.W.3    Li, Y.4
  • 92
    • 80053555277 scopus 로고    scopus 로고
    • Advancements in using reporter DNAzymes for identifying pathogenic bacteria at speed and with convenience
    • Li, Y., Advancements in using reporter DNAzymes for identifying pathogenic bacteria at speed and with convenience. Future Microbiol. 6 (2011), 973–976.
    • (2011) Future Microbiol. , vol.6 , pp. 973-976
    • Li, Y.1
  • 93
    • 84863759562 scopus 로고    scopus 로고
    • Detection of bacteria using fluorogenic DNAzymes
    • pii: 3961
    • Aguirre, S.D., Ali, M.M., Kanda, P., Li, Y., Detection of bacteria using fluorogenic DNAzymes. J. Vis. Exp., 2012 pii: 3961.
    • (2012) J. Vis. Exp.
    • Aguirre, S.D.1    Ali, M.M.2    Kanda, P.3    Li, Y.4
  • 94
    • 84870170959 scopus 로고    scopus 로고
    • Lighting up RNA-cleaving DNAzymes for biosensing
    • Tram, K., Kanda, P., Li, Y., Lighting up RNA-cleaving DNAzymes for biosensing. J. Nucleic Acids, 2012, 2012, 958683.
    • (2012) J. Nucleic Acids , vol.2012 , pp. 958683
    • Tram, K.1    Kanda, P.2    Li, Y.3
  • 95
    • 84979493600 scopus 로고    scopus 로고
    • A sensitive DNA enzyme-based fluorescent assay for bacterial detection
    • Aguirre, S.D., Ali, M.M., Salena, B.J., Li, Y., A sensitive DNA enzyme-based fluorescent assay for bacterial detection. Biomolecules 3 (2013), 563–577.
    • (2013) Biomolecules , vol.3 , pp. 563-577
    • Aguirre, S.D.1    Ali, M.M.2    Salena, B.J.3    Li, Y.4
  • 96
    • 84919800838 scopus 로고    scopus 로고
    • Examination of bacterial inhibition using a catalytic DNA
    • Qu, L., Ali, M.M., Aguirre, S.D., Liu, H., Jiang, Y., Li, Y., Examination of bacterial inhibition using a catalytic DNA. PLoS One, 9, 2014, e115640.
    • (2014) PLoS One , vol.9
    • Qu, L.1    Ali, M.M.2    Aguirre, S.D.3    Liu, H.4    Jiang, Y.5    Li, Y.6
  • 98
    • 0029905671 scopus 로고    scopus 로고
    • Fishing the best pool for novel ribozymes
    • Wedel, A.B., Fishing the best pool for novel ribozymes. Trends Biotechnol. 14 (1996), 459–465.
    • (1996) Trends Biotechnol. , vol.14 , pp. 459-465
    • Wedel, A.B.1
  • 100
    • 79952422304 scopus 로고    scopus 로고
    • Quality control and preprocessing of metagenomic datasets
    • Schmieder, R., Edwards, R., Quality control and preprocessing of metagenomic datasets. Bioinformatics 27 (2011), 863–864.
    • (2011) Bioinformatics , vol.27 , pp. 863-864
    • Schmieder, R.1    Edwards, R.2
  • 101
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li, W., Godzik, A., Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22 (2006), 1658–1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.