ATP-dependent allosteric DNA enzymes

Chemistry and Biology

Volumn 9, Issue 4, 2002, Pages 417-426

  Levy, Matthew ^a   Ellington, Andrew D ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; DEOXYRIBOZYME; LIGASE; OLIGODEOXYRIBONUCLEOTIDE;

ALLOSTERISM; ARTICLE; CATALYSIS; CHEMISTRY; CONFORMATION; DOSE RESPONSE; DRUG DESIGN; DRUG EFFECT; ENZYME ACTIVATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ADENOSINE TRIPHOSPHATE; ALLOSTERIC REGULATION; BASE SEQUENCE; CATALYSIS; DNA, CATALYTIC; DOSE-RESPONSE RELATIONSHIP, DRUG; DRUG DESIGN; ENZYME ACTIVATION; LIGASES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES;

EID: 0036236786     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(02)00123-0     Document Type: Article

References (58)

1. Crystal structure of a group I ribozyme domain: Principles of RNA packing
2. Structure-function relationships of hammerhead ribozymes: From understanding to applications
3. Deoxyribozymes: New players in the ancient game of biocatalysis
4. A DNA enzyme that cleaves RNA
5. In vitro selection of self-cleaving DNAs
6. Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme
7. Characterization and divalent metal-ion dependence of in vitro selected deoxyribozymes which cleave DNA/RNA chimeric oligonucleotides
8. A DNA metalloenzyme with DNA ligase activity
9. Phosphorylating DNA with DNA
10. Capping DNA with DNA
11. Rational design of allosteric ribozymes
12. Engineering precision RNA molecular switches
13. Design and optimization of effector-activated ribozyme ligases
14. In vitro Selection of Allosteric Ribozymes: Theory and Experimental Validation
15. An allosteric hammerhead ribozyme
16. In vitro selection of an allosteric ribozyme that transduces analytes to amplicons
17. Construction of new ribozymes requiring short regulator oligonucleotides as a cofactor
18. In vitro selection of nucleoprotein enzymes
19. Mechanism for allosteric inhibition of an ATP-sensitive ribozyme
20. Chemical and enzymatic probing of effector-mediated changes in the conformation of a maxizyme
21. A novel allosterically trans-activated ribozyme, the maxizyme, with exceptional specificity in vitro and in vivo
22. Nucleic acid molecular switches
23. An amino acid as a cofactor for a catalytic polynucleotide
24. A general purpose RNA-cleaving DNA enzyme
25. A novel mode of regulation of an RNA-cleaving DNAzyme by effectors that bind to both enzyme and substrate
26. In vitro selection of a deoxyribozyme that can utilize multiple substrates
27. Selection of deoxyribozyme ligases that catalyze the formation of an unnatural internucleotide linkage
28. A novel 5′-iodonucleoside allows efficient nonenzymic ligation of single-stranded and duplex DNAs
29. Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: Distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP
30. High sequence fidelity in a non-enzymatic DNA autoligation reaction
31. Stability and structure of three-way DNA junctions containing unpaired nucleotides
32. Conformational flexibility of three-way DNA junctions containing unpaired nucleotides
33. Solution structure of a DNA three-way junction containing two unpaired thymidine bases. Identification of sequence features that decide conformer selection
34. Structural features of a three-stranded DNA junction containing a C-C junctional bulge
35. Conformational differences between bulged pyrimidines (C-C) and purines (A-A, I-I) at the branch point of three-stranded DNA junctions
36. Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization
37. A DNA aptamer that binds adenosine and ATP
38. Allosteric regulation of a ribozyme activity through ligand-induced conformational change
39. Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP
40. Designed signaling aptamers that transduce molecular recognition to changes in fluorescence intensity
41. Quantitative analysis of receptors for adenosine nucleotides obtained via in vitro selection from a library incorporating a cationic nucleotide analog
42. Altering molecular recognition of RNA aptamers by allosteric selection
43. Cooperative binding of effectors by an allosteric ribozyme
44. Channeling of substrates and intermediates in enzyme-catalyzed reactions
45. HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA
46. High-resolution mapping of the human T-cell leukemia virus type 1 Rex-binding element by in vitro selection
47. The secondary structure and sequence optimization of an RNA ligase ribozyme
48. Optimization and optimality of a short ribozyme ligase that joins non-Watson-Crick base pairings
49. Directed evolution of a fungal peroxidase
50. Directed evolution of beta -glucosidase A from Paenibacillus polymyxa to thermal resistance
51. The determinants of alpha-amylase pH-activity profiles
52. Novel and variant ribozymes obtained through in vitro selection
53. In vitro selection of functional nucleic acids
54. Ribozyme Selection
55. Evolution of DNA and RNA as catalysts for chemical reactions
56. In vitro selection of nucleic acids for diagnostic applications
57. Immobilized RNA switches for the analysis of complex chemical and biological mixtures
58. Training ribozymes to switch