The structural diversity of deoxyribozymes

Molecules

Volumn 15, Issue 9, 2010, Pages 6269-6284

  McManus, Simon A ^a   Li, Yingfu ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

Catalytic DNA; Deoxyribozyme; DNAzyme; Functional nucleic acid; In vitro selection

Indexed keywords

DEOXYRIBOZYME; PHOSPHOTRANSFERASE;

CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; METABOLISM; MUTAGENESIS; REVIEW; STRUCTURE ACTIVITY RELATION;

DNA, CATALYTIC; MOLECULAR STRUCTURE; MUTAGENESIS; NUCLEIC ACID CONFORMATION; PHOSPHOTRANSFERASES; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77957307747     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules15096269     Document Type: Review

References (77)

1. Zaug, A. J.; Grabowski, P. J.; Cech, T. R. Autocatalytic cyclization of an excised intervening sequence RNA is a cleavage-ligation reaction. Nature 1983, 301, 578-583.
2. Forster, A. C.; Symons, R. H. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell 1987, 49, 211-220.
3. Feldstein, P. A.; Buzayan, J. M.; Bruening, G. Two sequences participating in the autolytic processing of satellite tobacco ringspot virus complementary RNA. Gene 1989, 82, 53-61.
4. Beattie, T. L.; Olive, J. E.; Collins, R. A. A secondary-structure model for the self-cleaving region of Neurospora VS RNA. Proc. Natl. Acad. Sci. USA 1995, 92, 4686-4690.
5. Been, M. D. Cis- and trans-acting ribozymes from a human pathogen, hepatitis delta virus. Trends Biochem. Sci. 1994, 19, 251-256.
6. Guerrier-Takada, C.; Gardiner, K.; Marsh, T.; Pace, N.; Altman, S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 1983, 35, 849-857.
7. Joyce, G. F. The antiquity of RNA-based evolution. Nature 2002, 418, 214-221.
8. Joyce, G. F. Forty years of in vitro evolution. Angew. Chem. Int. Ed. 2007, 46, 6420-6436.
9. Chapman, K. B.; Szostak, J. W. In vitro selection of catalytic RNAs. Curr. Opin. Struct. Biol. 1994, 4, 618-622.
10. Breaker, R. R.; Joyce, G. F. A DNA enzyme that cleaves RNA. Chem. Biol. 1994, 1, 223-229.
11. Silverman, S. K. Catalytic DNA (deoxyribozymes) for synthetic applications-current abilities and future prospects. Chem. Commun. 2008, 3467-3485.
12. Baum, D. A.; Silverman, S. K. Deoxyribozymes: useful DNA catalysts in vitro and in vivo. Cell. Mol. Life Sci. 2008, 65, 2156-2174.
13. Sen, D.; Geyer, C. R. DNA enzymes. Curr. Opin. Chem. Biol. 1998, 2, 680-687.
14. Cuenoud, B.; Szostak, J. W. A DNA metalloenzyme with DNA ligase activity. Nature 1995, 375, 611-614.
15. Sreedhara, A.; Li, Y.; Breaker, R. R. Ligating DNA with DNA. J. Am. Chem. Soc. 2004, 126, 3454-3460.
16. Flynn-Charlebois, A.; Wang, Y.; Prior, T. K.; Rashid, I.; Hoadley, K. A.; Coppins, R. L.; Wolf, A. C.; Silverman, S. K. Deoxyribozymes with 2′-5′ RNA ligase activity. J. Am. Chem. Soc. 2003, 125, 2444-2454.
17. Purtha, W. E.; Coppins, R. L.; Smalley, M. K.; Silverman, S. K. General deoxyribozyme-catalyzed synthesis of native 3′-5′ RNA linkages. J. Am. Chem. Soc. 2005, 127, 13124-13125.
18. Pratico, E. D.; Wang, Y.; Silverman, S. K. A deoxyribozyme that synthesizes 2′, 5′-branched RNA with any branch-site nucleotide. Nucleic Acids Res. 2005, 33, 3503-3512.
19. Li, Y.; Breaker, R. R. Phosphorylating DNA with DNA. Proc. Natl. Acad. Sci. USA 1999, 96, 2746-2751.
20. Wang, W.; Billen, L. P.; Li, Y. Sequence diversity, metal specificity, and catalytic proficiency of metal-dependent phosphorylating DNA enzymes. Chem. Biol. 2002, 9, 507-517.
21. Li, Y.; Liu, Y.; Breaker, R. R. Capping DNA with DNA. Biochemistry 2000, 39, 3106-3114.
22. Carmi, N.; Balkhi, S. R.; Breaker, R. R. Cleaving DNA with DNA. Proc. Natl. Acad. Sci. U. S. A. 1998, 95, 2233-2237.
23. Chandra, M.; Sachdeva, A.; Silverman, S. K. DNA-catalyzed sequence-specific hydrolysis of DNA. Nat. Chem. Biol. 2009, 5, 718-720.
24. Li, Y.; Sen, D. A catalytic DNA for porphyrin metallation. Nat. Struct. Biol. 1996, 3, 743-747.
25. Chinnapen, D. J.; Sen, D. A deoxyribozyme that harnesses light to repair thymine dimers in DNA. Proc. Natl. Acad. Sci. USA 2004, 101, 65-69.
26. Pradeepkumar, P. I.; Hobartner, C.; Baum, D. A.; Silverman, S. K. DNA-catalyzed formation of nucleopeptide linkages. Angew. Chem. Int. Ed. 2008, 47, 1753-1757.
27. Chandra, M.; Silverman, S. K. DNA and RNA can be equally efficient catalysts for carbon-carbon bond formation. J. Am. Chem. Soc. 2008, 130, 2936-2937.
28. Maxam, A. M.; Gilbert, W. A new method for sequencing DNA. Proc. Natl. Acad. Sci. U. S. A. 1977, 74, 560-564.
29. Sanger, F.; Nicklen, S.; Coulson, A. R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 1977, 74, 5463-5467.
30. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31, 3406-3415.
31. Beal, P. A.; Dervan, P. B. Second structural motif for recognition of DNA by oligonucleotidedirected triple-helix formation. Science 1991, 251, 1360-1363.
32. Aboul-ela, F.; Murchie, A. I.; Lilley, D. M. NMR study of parallel-stranded tetraplex formation by the hexadeoxynucleotide d (TG4T). Nature 1992, 360, 280-282.
33. Phan, A. T.; Mergny, J. L. Human telomeric DNA: G-quadruplex, i-motif and Watson-Crick double helix. Nucleic Acids Res. 2002, 30, 4618-4625.
34. Feldman, A. R.; Sen, D. A new and efficient DNA enzyme for the sequence-specific cleavage of RNA. J. Mol. Biol. 2001, 313, 283-294.
35. Breaker, R. R.; Joyce, G. F. A DNA enzyme with Mg (2+)-dependent RNA phosphoesterase activity. Chem. Biol. 1995, 2, 655-660.
36. 2+ ion as a cofactor for a novel RNA-cleaving deoxyribozyme. Angew. Chem. Int. Ed. 1996, 35, 2809-2813.
37. Santoro, S. W.; Joyce, G. F. A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. USA 1997, 94, 4262-4266.
38. Geyer, C. R.; Sen, D. Evidence for the metal-cofactor independence of an RNA phosphodiestercleaving DNA enzyme. Chem. Biol. 1997, 4, 579-593.
39. 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. 2004, 32, 1591-1601.
40. Hollenstein, M.; Hipolito, C. J.; Lam, C. H.; Perrin, D. M. A self-cleaving DNA enzyme modified with amines, guanidines and imidazoles operates independently of divalent metal cations (M2+). Nucleic Acids Res. 2009, 37, 1638-1649.
41. Perrin, D. M.; Garestier, T.; Helene, C. Bridging the gap between proteins and nucleic acids: a metal-independent RNAseA mimic with two protein-like functionalities. J. Am. Chem. Soc. 2001, 123, 1556-1563.
42. Ting, R.; Thomas, J. M.; Lermer, L.; Perrin, D. M. Substrate specificity and kinetic framework of a DNAzyme with an expanded chemical repertoire: a putative RNaseA mimic that catalyzes RNA hydrolysis independent of a divalent metal cation. Nucleic Acids Res. 2004, 32, 6660-6672.
43. Silverman, S. K. In vitro selection, characterization, and application of deoxyribozymes that cleave RNA. Nucleic Acids Res. 2005, 33, 6151-6163.
44. Peracchi, A.; Bonaccio, M.; Clerici, M. A mutational analysis of the 8-17 deoxyribozyme core. J. Mol. Biol. 2005, 352, 783-794.
45. Cruz, R. P.; Withers, J. B.; Li, Y. Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme. Chem. Biol. 2004, 11, 57-67.
46. Zaborowska, Z.; Schubert, S.; Kurreck, J.; Erdmann, V. A. Deletion analysis in the catalytic region of the 10-23 DNA enzyme. FEBS Lett. 2005, 579, 554-558.
47. Zaborowska, Z.; Furste, J. P.; Erdmann, V. A.; Kurreck, J. Sequence requirements in the catalytic core of the "10-23" DNA enzyme. J. Biol. Chem. 2002, 277, 40617-40622.
48. Li, J.; Zheng, W.; Kwon, A. H.; Lu, Y. In vitro selection and characterization of a highly efficient Zn (II)-dependent RNA-cleaving deoxyribozyme. Nucleic Acids Res. 2000, 28, 481-488.
49. Peracchi, A. 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. 2000, 275, 11693-11697.
50. Sheppard, T. L.; Ordoukhanian, P.; Joyce, G. F. A DNA enzyme with N-glycosylase activity. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 7802-7807.
51. Chiuman, W.; Li, Y. Evolution of high-branching deoxyribozymes from a catalytic DNA with a three-way junction. Chem. Biol. 2006, 13, 1061-1069.
52. Morgan, A. R.; Wells, R. D. Specificity of the three-stranded complex formation between doublestranded DNA and single-stranded RNA containing repeating nucleotide sequences. J. Mol. Biol. 1968, 37, 63-80.
53. Wells, R. D.; Collier, D. A.; Hanvey, J. C.; Shimizu, M.; Wohlrab, F. The chemistry and biology of unusual DNA structures adopted by oligopurine. oligopyrimidine sequences. FASEB J. 1988, 2, 2939-2949.
54. Gellert, M.; Lipsett, M. N.; Davies, D. R. Helix formation by guanylic acid. Proc. Natl. Acad. Sci. U. S. A. 1962, 48, 2013-2018.
55. Arnott, S.; Chandrasekaran, R.; Marttila, C. M. Structures for polyinosinic acid and polyguanylic acid. Biochem. J. 1974, 141, 537-543.
56. Williamson, J. R.; Raghuraman, M. K.; Cech, T. R. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell 1989, 59, 871-880.
57. Wang, Y.; Patel, D. J. Solution structure of a parallel-stranded G-quadruplex DNA. J. Mol. Biol. 1993, 234, 1171-1183.
58. Huppert, J. L.; Balasubramanian, S. G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res. 2007, 35, 406-413.
59. Li, Y.; Sen, D. Toward an efficient DNAzyme. Biochemistry 1997, 36, 5589-5599.
60. Lilley, D. M. Structure, folding and mechanisms of ribozymes. Curr. Opin. Struct. Biol. 2005, 15, 313-323.
61. Chen, X.; Li, N.; Ellington, A. D. Ribozyme catalysis of metabolism in the RNA world. Chem. Biodivers. 2007, 4, 633-655.
62. Beaudoin, J. D.; Perreault, J. P. Potassium ions modulate a G-quadruplex-ribozyme's activity. RNA 2008, 14, 1018-1025.
63. Wieland, M.; Hartig, J. S. Turning inhibitors into activators: a hammerhead ribozyme controlled by a guanine quadruplex. Angew. Chem. Int. Ed. 2006, 45, 5875-5878.
64. Travascio, P.; Bennet, A. J.; Wang, D. Y.; Sen, D. A ribozyme and a catalytic DNA with peroxidase activity: active sites versus cofactor-binding sites. Chem. Biol. 1999, 6, 779-787.
65. Joachimi, A.; Benz, A.; Hartig, J. S. A comparison of DNA and RNA quadruplex structures and stabilities. Bioorg. Med. Chem. 2009, 17, 6811-6815.
66. Neidle, S.; Balasubramanian, S. Quadruplex Nucleic Acids; Royal Society of Chemistry: London, UK, 2006.
67. Bloomfield, V. A.; Crothers, D. M.; Tinoco, I. Nucleic Acids: Structures, Properties, and Functions; University Science Books: Sausalito, CA, USA, 2000.
68. Liu, Z.; Mei, S. H.; Brennan, J. D.; Li, Y. Assemblage of signaling DNA enzymes with intriguing metal-ion specificities and pH dependences. J. Am. Chem. Soc. 2003, 125, 7539-7545.
69. Shen, Y.; Brennan, J. D.; Li, Y. Characterizing the secondary structure and identifying functionally essential nucleotides of pH6DZ1, a fluorescence-signaling and RNA-cleaving deoxyribozyme. Biochemistry 2005, 44, 12066-12076.
70. Kandadai, S. A.; Mok, W. W.; Ali, M. M.; Li, Y. Characterization of an RNA-cleaving deoxyribozyme with optimal activity at pH 5. Biochemistry 2009, 48, 7383-7391.
71. Kandadai, S. A.; Li, Y. Characterization of a catalytically efficient acidic RNA-cleaving deoxyribozyme. Nucleic Acids Res. 2005, 33, 7164-7175.
72. Ali, M. M.; Kandadai, S. A.; Li, Y. Characterization of pH3DZ1 - An RNA-cleaving deoxyribozyme with optimal activity at pH 3. Can. J. Chem. 2007, 85, 261-273.
73. Achenbach, J. C.; Jeffries, G. A.; McManus, S. A.; Billen, L. P.; Li, Y. Secondary-structure characterization of two proficient kinase deoxyribozymes. Biochemistry 2005, 44, 3765-3774.
74. McManus, S. A.; Li, Y. Multiple occurrences of an efficient self-phosphorylating deoxyribozyme motif. Biochemistry 2007, 46, 2198-2204.
75. McManus, S. A.; Li, Y. A deoxyribozyme with a novel guanine quartet-helix pseudoknot structure. J. Mol. Biol. 2008, 375, 960-968.
76. Sabeti, P. C.; Unrau, P. J.; Bartel, D. P. Accessing rare activities from random RNA sequences: the importance of the length of molecules in the starting pool. Chem. Biol. 1997, 4, 767-774.
77. Gevertz, J.; Gan, H. H.; Schlick, T. In vitro RNA random pools are not structurally diverse: a computational analysis. RNA 2005, 11, 853-863.