Deoxyribozymes: New activities and new applications

Cellular and Molecular Life Sciences

Volumn 59, Issue 4, 2002, Pages 596-607

  Emilsson, G M ^a   Breaker, R R ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Catalytic DNA; Deoxyribozyme; In vitro selection; Nucleic acid catalysis; Ribozyme; RNA cleavage

Indexed keywords

DEOXYRIBOZYME; DNA; RIBOZYME;

ADENYLATION; BIOSENSOR; CATALYSIS; CHEMICAL REACTION; DNA DEGRADATION; DNA HELIX; ENZYME ACTIVITY; MOLECULAR RECOGNITION; OXIDATION REDUCTION REACTION; REVIEW; RNA CLEAVAGE;

ANIMALS; BASE SEQUENCE; BIOTECHNOLOGY; DNA; DNA, CATALYTIC; GENOME; KINETICS; METALS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; RNA;

EID: 0036240768     PISSN: 1420682X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00018-002-8452-4     Document Type: Review

References (77)

1. Ribonuclease P: Unity and diversity in a rRNA processing ribozyme
2. The structural basis of ribosome activity in peptide bond synthesis
3. Synthetic ribozymes and the first deoxyribozyme
4. DNA Enzymes
5. DNA aptamers and DNA enzymes
6. Deoxyribozymes: New players in the ancient game of biocatalysis
7. Catalytic DNA: In training and seeking employment
8. Evolution of DNA and RNA as catalysts for chemical reactions
9. Making catalytic DNAs
10. The RNA world
11. Prospects for understanding the origin of the RNA world
12. In vitro selection of catalytic polynucleotides
13. The new world of ribozymes
14. In vitro selection of functional nucleic acids
15. Crystal structure of a group I ribozyme domain: Principles of RNA packing
16. RNA folds: Insights from recent crystal structures
17. Catalytic DNAs as potential therapeutic agents and sequence-specific molecular tools to dissect biological function
18. Catalytic nucleic acids: From lab to applications
19. Using DNAzymes to cut, process and map RNA molecules for structural studies or modification
20. RNA-catalysed nucleotide synthesis
21. Homogeneous assays based on deoxyribozyme catalysis
22. Catalytic molecular beacons
23. A novel mode of regulation of an RNA-cleaving DNAzyme by effectors that bind to both enzyme and substrate
24. DzyNA-PCR: Use of DNAzymes to detect and quantify nucleic acid sequences in a real-time fluorescent format
25. A highly sensitive and selective catalytic DNA biosensor for lead ions
26. Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme
27. An amino acid as a cofactor for a catalytic polynucleotide
28. A DNA enzyme that cleaves RNA
29. Building a catalytic active site using only RNA
30. A general purpose RNA-cleaving DNA enzyme
31. Mechanism and utility of an RNA-cleaving DNA enzyme
32. Targeted cleavage of HIV-1 coreceptor-CXCR-4 by RNA-cleaving DNA-enzyme: Inhibition of coreceptor function
33. Inhibition of influenza virus replication in cultured cells by RNA-cleaving DNA enzyme
34. In vitro-selected RNA cleaving DNA enzymes from a combinatorial library are potent inhibitors of HIV-1 gene expression
35. New DNA enzyme targeting Egr-1 mRNA inhibits vascular smooth muscle proliferation and regrowth after injury
36. Progress in antisense technology: The end of the beginning
37. 2+-dependent RNA phosphoesterase activity
38. Allosteric nucleic acid catalysts
39. Immobilized RNA switches for the analysis of complex chemical and biological mixtures
40. Nucleic acid enzymes: Playing with a fuller deck
41. RNA cleavage by a DNA enzyme with extended chemical functionality
42. Kinetics of RNA degradation by specific base catalysis of transesterfication involving the 2′-hydroxyl group
43. Bridging the gap between proteins and nucleic acids: A metal-independent RNase A mimic with two protein-like functionalities
44. A proficient enzyme
45. Instability and decay of the primary structure of DNA
46. Chemical nucleases
47. DNA enzymes: New-found chemical reactivity
48. In vitro selection of self-cleaving DNAs
49. Cleaving DNA with DNA
50. Characterization of a DNA-cleaving deoxyribozyme
51. DNA cleavage by Cu(II)-desferal: Identification of C1′-hydroxylation as the initial event for DNA damage
52. A DNA enzyme with N-glycosylase activity
53. Cofactor-assisted self-cleavage in DNA libraries with a 3′-5′ phosphoramidate bond
54. A catalytic DNA for porphyrin metallation
55. The modus operandi of a DNA enzyme: Enhancement of substrate basicity
56. A ribozyme and a catalytic DNA with peroxidase activity: Active sites versus cofactor-binding sites
57. Isolation of a fluorophorespecific DNA aptamer with weak redox activity
58. Phosphorylating DNA with DNA
59. In vitro selection of new ribozymes with polynucleotide kinase activity
60. DNA ligase: Structure, mechanism, and function
61. Capping DNA with DNA
62. 5′-RNA self-capping from guanosine diphosphate
63. A DNA metalloenzyme with ligase activity
64. 2+ on complex formation between a deoxyribozyme and its substrates
65. Selection of deoxyribozyme ligases that catalyze the formation of an unnatural internucleotide linkage
66. Crystal structure of an 82-nucleotide RNA-DNA complex formed by the 10-23 DNA enzyme
67. Effect of metal ions and sequence of deoxyribozymes on their RNA cleavage activity
68. Effects of metal ions and catalytic loop sequences on the complex formation of a deoxyribozyme and its RNA substrate
69. RNA structure at high resolution
70. Stitching together RNA tertiary architectures
71. Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function
72. 2+ ion as a co-factor for a novel RNA-cleaving deoxyribozyme
73. Characterization and divalent metal-ion dependence of in vitro selected deoxyribozymes which cleave DNA/RNA chimeric oligonucleotides
74. In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme
75. 2+ ions: Evidence for the identity of 8-17 with the catalytic domain of the Mg5 deoxyribozyme
76. Toward an efficient DNAzyme