Rational evolution of Cd2+-specific DNAzymes with phosphorothioate modified cleavage junction and Cd2+ sensing

Nucleic Acids Research

Volumn 43, Issue 12, 2015, Pages 6125-6133

  Huang, Po Jung Jimmy ^a   Liu, Juewen ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CADMIUM; DEOXYRIBOZYME; NUCLEOTIDE; ZINC; OLIGONUCLEOTIDE PHOSPHOROTHIOATE;

ARTICLE; BINDING SITE; CATALYSIS; CONTROLLED STUDY; DNA BINDING; DNA CLEAVAGE; DNA DETERMINATION; DNA LIBRARY; DNA MODIFICATION; DNA STRUCTURE; IN VITRO SELECTION; METAL BINDING; NONHUMAN; PRIORITY JOURNAL; CHEMISTRY; CONFORMATION; DIRECTED MOLECULAR EVOLUTION; GENE LIBRARY; GENETIC PROCEDURES; METABOLISM; ORYZA; RNA CLEAVAGE; STEREOISOMERISM;

BINDING SITES; BIOSENSING TECHNIQUES; CADMIUM; DIRECTED MOLECULAR EVOLUTION; DNA, CATALYTIC; GENE LIBRARY; NUCLEIC ACID CONFORMATION; ORYZA; PHOSPHOROTHIOATE OLIGONUCLEOTIDES; RNA CLEAVAGE; STEREOISOMERISM;

EID: 84942134173     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv519     Document Type: Article

References (112)

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36. Deleavey, G.F. and Damha, M.J. (2012) Designing chemically modified oligonucleotides for targeted gene silencing. Chem. Biol, 19, 937-954.
37. Lee, J.H., Wernette, D.P, Yigit, M.V., Liu, J., Wang, Z. and Lu, Y. (2007) Site-specific control of distances between gold nanoparticles using phosphorothioate anchors on DNA and a short bifunctional molecular fastener. Angew. Chem. Int. Ed., 46, 9006-9010.
38. Pal, S., Sharma, J., Yan, H. and Liu, Y (2009) Stable silver nanoparticle-DNA conjugates for directed self-assembly of core-satellite silver-gold nanoclusters. Chem. Commun., 45, 6059-6061.
39. Kumar, A., Phadtare, S., Pasricha, R., Guga, P, Ganesh, K.N and Sastry, M. (2003) Assembling gold nanoparticles in solution using phosphorothioate DNA as structural interconnects. Curr Sci., 84, 71-74.
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41. Ma, N, Sargent, E.H. and Kelley, S.O. (2009) One-step DNA-programmed growth of luminescent and biofunctionalized nanocrystals. Nat. Nanotechnol., 4, 121-125.
42. Jarup, L. (2003) Hazards of heavy metal contamination. Br. Med. Bull, 68, 167-182.
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44. Kim, HN, Ren, W.X., Kim, J.S. and Yoon, J. (2012) Fluorescent and colorimetric sensors for detection of lead, cadmium, and mercury ions. Chem. Soc. Rev., 41, 3210-3244.
45. 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.
46. Santoro, S.W. and Joyce, GF (1997) A general purpose RNA-cleaving DNA enzyme. Proc Natl. Acad. Sci. U.S.A., 94, 4262-4266.
47. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
48. Ora, M., Peltomaki, M., Oivanen, M. and Lonnberg, H. (1998) Metal-ion-promoted cleavage, isomerization, and desulfurization of the diastereomeric phosphoromonothioate analogues of uridylyl(3',5')uridine. J. Org. Chem., 63, 2939-2947.
49. Thaplyal, P, Ganguly, A., Golden, B.L., Hammes-Schiffer, S. and Bevilacqua, PC (2013) Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme. Biochemistry, 52, 6499-6514.
50. 2+ -ribozyme by a single rp-phosphorothioate modification in the precursor trna at the RNase P cleavage site. Proc. Natl. Acad. Sci. U.S.A., 93, 8924-8928.
51. p phosphorothioate substitution at the scissile site on the cleavage activity of deoxyribozyme 10-23. Curr. Org. Chem., 12, 1004-1009.
52. Sekhon, G.S. and Sen, D. (2010) A stereochemical glimpse of the active site of the 8-17 deoxyribozyme from iodine-mediated cross-links formed with the substrate's scissile site. Biochemistry, 49, 9072-9077.
53. Moore, M.J. and Sharp, PA. (1993) Evidence for two active sites in the spliceosome provided by stereochemistry of pre-mRNA splicing. Nature, 365, 364-368.
54. Schlosser, K., Gu, J, Sule, L. and Li, YF (2008) Sequence-function relationships provide new insight into the cleavage site selectivity of the 8-17 RNA-cleaving deoxyribozyme. Nucleic Acids Res, 36, 1472-1481.
55. Sczepanski, J.T. and Joyce, G.F (2014) A cross-chiral RNA polymerase ribozyme. Nature, 515, 440-442.
56. Wang, B., Cao, L., Chiuman, W., Li Y. and Xi, Z. (2010) Probing the function of nucleotides in the catalytic cores of the 8-17 and 10-23 dnazymes by abasic nucleotide and C3 spacer substitutions. Biochemistry, 49, 7553-7562.
57. Erkkila, K.E., Odom, D.T. and Barton, J.K. (1999) Recognition and reaction of metallointercalators with DNA. Chem. Rev., 99, 2777-2796.
58. Lu, Y. (2006) Metalloprotein and metallo-DNA/RNAzyme design: current approaches, success measures, and future challenges. Inorg. Chem., 45, 9930-9940.
59. Ward, W.L., Plakos, K. and DeRose, V.J. (2014) Nucleic acid catalysis: metals, nucleobases, and other cofactors. Chem. Rev., 114, 4318-4342.
60. Sigel, H. and Griesser, R. (2005) Nucleoside 5'-triphosphates: self-association, acid-base, and metal ion-binding properties in solution. Chem. Soc. Rev., 34, 875-900.
61. Sigel, R.K.O. and Sigel, H. (2010) A stability concept for metal ion coordination to single-stranded nucleic acids and affinities of individual sites. Acc. Chem. Res., 43, 974-984.
62. Jamieson, E.R. and Lippard, S.J. (1999) Structure, recognition, and processing of cisplatin-DNA adducts. Chem. Rev., 99, 2467-2498.
63. Zhang, X.-B., Kong, R.-M. and Lu, Y. (2011) Metal ion sensors based on DNAzymes and related DNA molecules. Annu. Rev. Anal. Chem., 4, 105-128.
64. Sigel, R.K.O. and Pyle, A.M. (2007) Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry. Chem. Rev, 107, 97-113.
65. Liu, J., Cao, Z. and Lu, Y. (2009) Functional nucleic acid sensors. Chem. Rev, 109, 1948-1998.
66. Schlosser, K. and Li, Y.F. (2009) Biologically inspired synthetic enzymes made from DNA. Chem. Biol, 16, 311-322.
67. Schlosser, K. and Li, Y. (2010) A versatile endoribonuclease mimic made of DNA: characteristics and applications of the 8-17 RNA-cleaving DNAzyme. ChemBioChem, 11, 866-879.
68. Lu, Y (2002) New transition metal-dependent dnazymes as efficient endonucleases and as selective metal biosensors. Chem. Eur. J., 8, 4588-4596.
69. Breaker, R.R. (1997) DNA enzymes. Nat. Biotechnol, 15, 427-431.
70. Silverman, S.K. (2009) Deoxyribozymes: selection design and serendipity in the development of DNA catalysts. Acc. Chem. Res., 42, 1521-1531.
71. Famulok, M., Hartig, J.S. and Mayer, G. (2007) Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem. Rev, 107, 3715-3743.
72. Sen, D and Geyer, C.R. (1998) DNA enzymes. Curr. Opin. Chem. Biol, 2, 680-687.
73. Breaker, R.R. and Joyce, G.F (1994) A DNA enzyme that cleaves RNA. Chem. Biol, 1, 223-229.
74. Li, J. and Lu, Y (2000) A highly sensitive and selective catalytic DNA biosensor for lead ions. J. Am. Chem. Soc, 122, 10466-10467.
75. Brown, A.K., Li, J., Pavot, C.M.B. and Lu, Y (2003) A lead-dependent DNAzyme with a two-step mechanism. Biochemistry, 42, 7152-7161.
76. Liu, J., Brown, A.K., Meng, X., Cropek, D.M., Istok, J.D, Watson, DB. and Lu, Y (2007) A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity. Proc Natl Acad. Sci. U.S.A., 104, 2056-2061.
77. Cepeda-Plaza, M., Null, E.L. and LuY. (2013) Metal ion as both a cofactor and a probe of metal-binding sites in a uranyl-specific DNAzyme: a uranyl photocleavage study. Nucleic Acids Res., 41, 9361-9370.
78. Huang, P.-J.J, Lin, J., Cao, J., Vazin, M. and Liu, J. (2014) Ultrasensitive DNAzyme beacon for lanthanides and metal speciation. Anal. Chem., 86, 1816-1821.
79. Huang, P-J.J., Vazin, M. and Liu, J. (2014) In vitro selection of a new lanthanide-dependent DNAzyme for ratiometric sensing lanthanides. Anal. Chem., 86, 9993-9999.
80. Huang, P-J.J., Vazin, M., Matuszek, Z. and Liu, J. (2015) A new heavy lanthanide-dependent DNAzyme displaying strong metal cooperativity and unrescuable phosphorothioate effect. Nucleic Acids Res., 43, 461-469.
81. 2+ ions resulting in variants of DNAzyme 8-17. Dalton Trans., 44, 8138-8149.
82. Santoro, S.W., Joyce, G.F, Sakthivel, K., Gramatikova, S. and Barbas, C.F III (2000) RNA cleavage by a DNA enzyme with extended chemical functionality. J. Am. Chem. Soc, 122, 2433-2439.
83. Hollenstein, M., Hipolito, C, Lam, C, Dietrich, D. and Perrin, DM. (2008) A highly selective DNAzyme sensor for mercuric ions. Angew. Chem. Int. Ed., 47, 4346-4350.
84. Lermer, L., Roupioz, Y, Ting, R. and Perrin, DM. (2002) Toward an rnasea mimic: a DNAzyme with imidazoles and cationic amines. J. Am. Chem. Soc, 124, 9960-9961.
85. Li, M.Y., Lin, N, Huang, Z., Du, L.P, Altier, C, Fang, H. and Wang, B.H. (2008) Selecting aptamers for a glycoprotein through the incorporation of the boronic acid moiety. J. Am. Chem. Soc., 130, 12636-12637.
86. Frederiksen, J.K. and Piccirilli, J.A. (2009) Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding: Part A. Meth. Enzymol, 468, 289-309.
87. Song, B., Sigel, R.K.O. and Sigel, H. (1997) Acid-base properties of adenosine 5'-O-thiomonophosphate in aqueous solution. Chem. Eur. J., 3, 29-33.
88. Wang, S., Karbstein, K., Peracchi, A., Beigelman, L. and Herschlag, D. (1999) Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate. Biochemistry, 38, 14363-14378.
89. Nawrot, B., Widera, K., Wojcik, M., Rebowska, B., Nowak, G. and Stec, W.J. (2007) Mapping of the functional phosphate groups in the catalytic core of deoxyribozyme 10-23. FEBS J., 274, 1062-1072.
90. Cunningham, L.A., Li, J. and Lu, Y. (1998) Spectroscopic evidence for inner-sphere coordination of metal ions to the active site of a hammerhead ribozyme. J. Am. Chem. Soc, 120, 4518-4519.
91. 2+ collectively and individually using phosphorothioate dnazymes. Anal. Chem., 86, 5999-6005.
92. Deleavey, G.F. and Damha, M.J. (2012) Designing chemically modified oligonucleotides for targeted gene silencing. Chem. Biol, 19, 937-954.
93. Lee, J.H., Wernette, D.P, Yigit, M.V., Liu, J., Wang, Z. and Lu, Y. (2007) Site-specific control of distances between gold nanoparticles using phosphorothioate anchors on DNA and a short bifunctional molecular fastener. Angew. Chem. Int. Ed., 46, 9006-9010.
94. Pal, S., Sharma, J., Yan, H. and Liu, Y (2009) Stable silver nanoparticle-DNA conjugates for directed self-assembly of core-satellite silver-gold nanoclusters. Chem. Commun., 45, 6059-6061.
95. Kumar, A., Phadtare, S., Pasricha, R., Guga, P, Ganesh, K.N and Sastry, M. (2003) Assembling gold nanoparticles in solution using phosphorothioate DNA as structural interconnects. Curr Sci., 84, 71-74.
96. Farlow, J., Seo, D, Broaders, K.E., Taylor, M.J., Gartner, Z.J. and Jun, Y-w (2013) Formation of targeted monovalent quantum dots by steric exclusion. Nat. Methods, 10, 1203-1205.
97. Ma, N, Sargent, E.H. and Kelley, S.O. (2009) One-step DNA-programmed growth of luminescent and biofunctionalized nanocrystals. Nat. Nanotechnol., 4, 121-125.
98. Jarup, L. (2003) Hazards of heavy metal contamination. Br. Med. Bull, 68, 167-182.
99. Zhuang, P, McBride, M.B., Xia, H.P, Li, NY and Lia, Z.A. (2009) Health risk from heavy metals via consumption of food crops in the vicinity of dabaoshan mine, south China. Sci. Total Environ., 407, 1551-1561.
100. Kim, HN, Ren, W.X., Kim, J.S. and Yoon, J. (2012) Fluorescent and colorimetric sensors for detection of lead, cadmium, and mercury ions. Chem. Soc. Rev., 41, 3210-3244.
101. 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.
102. Santoro, S.W. and Joyce, GF (1997) A general purpose RNA-cleaving DNA enzyme. Proc Natl. Acad. Sci. U.S.A., 94, 4262-4266.
103. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
104. Ora, M., Peltomaki, M., Oivanen, M. and Lonnberg, H. (1998) Metal-ion-promoted cleavage, isomerization, and desulfurization of the diastereomeric phosphoromonothioate analogues of uridylyl(3',5')uridine. J. Org. Chem., 63, 2939-2947.
105. Thaplyal, P, Ganguly, A., Golden, B.L., Hammes-Schiffer, S. and Bevilacqua, PC (2013) Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme. Biochemistry, 52, 6499-6514.
106. 2+ -ribozyme by a single rp-phosphorothioate modification in the precursor trna at the RNase P cleavage site. Proc. Natl. Acad. Sci. U.S.A., 93, 8924-8928.
107. p phosphorothioate substitution at the scissile site on the cleavage activity of deoxyribozyme 10-23. Curr. Org. Chem., 12, 1004-1009.
108. Sekhon, G.S. and Sen, D. (2010) A stereochemical glimpse of the active site of the 8-17 deoxyribozyme from iodine-mediated cross-links formed with the substrate's scissile site. Biochemistry, 49, 9072-9077.
109. Moore, M.J. and Sharp, PA. (1993) Evidence for two active sites in the spliceosome provided by stereochemistry of pre-mRNA splicing. Nature, 365, 364-368.
110. Schlosser, K., Gu, J, Sule, L. and Li, YF (2008) Sequence-function relationships provide new insight into the cleavage site selectivity of the 8-17 RNA-cleaving deoxyribozyme. Nucleic Acids Res, 36, 1472-1481.
111. Sczepanski, J.T. and Joyce, G.F (2014) A cross-chiral RNA polymerase ribozyme. Nature, 515, 440-442.
112. Wang, B., Cao, L., Chiuman, W., Li Y. and Xi, Z. (2010) Probing the function of nucleotides in the catalytic cores of the 8-17 and 10-23 dnazymes by abasic nucleotide and C3 spacer substitutions. Biochemistry, 49, 7553-7562.