DNA aptamers and DNA enzymes

Current Opinion in Chemical Biology

Volumn 1, Issue 1, 1997, Pages 26-31

  Breaker, Ronald R ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOPOLYMER; DNA; DNA BINDING PROTEIN; ENZYME;

CATALYSIS; CHEMISTRY; CONFORMATION; METABOLISM; NUCLEOTIDE SEQUENCE; REVIEW; SYNTHESIS;

BASE SEQUENCE; BIOPOLYMERS; CATALYSIS; DNA; DNA-BINDING PROTEINS; ENZYMES; NUCLEIC ACID CONFORMATION;

EID: 0031151976     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/s1367-5931(97)80105-6     Document Type: Article

References (27)

1. Gold L, Polisky B, Uhlenbeck O, Yarus M: Diversity of oligonucleotide function. Annu Rev Biochem 1995, 64:763-797.
2. Gold L: Oligonucleotides as research, diagnostic, and therapeutic agents. J Biol Chem 1995, 270:13581-13584.
3. Ellington AD, Szostak JW: In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346:818-822.
4. Breaker RR: Are engineered proteins getting competition from RNA? Curr Opin Biotechnol 1996, 7:442-448.
5. Burgstaller P, Famulok M: Synthetic ribozymes and the first deoxyribozyme. Angew Chem Int Ed 1995, 34:1189-1192.
6. Breaker RR: In vitro selection of catalytic polynucleotides. Chem Rev 1997, in press.
7. Tuerk C, Gold L: Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249:505-510.
8. Corey MJ, Corey E: On the failure of de novo-designed peptides as biocatalysts. Proc Natl Acad Sci USA 1996, 93:11428-11434.
9. Bock LC, Griffin LC, Latham JA, Vermaas EH, Toole JJ: Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 1992, 355:564-566.
10. Macaya RF, Waldron JA, Beutel BA, Gao H, Joesten ME, Yang M, Patel R, Bertelsen AH, Cook AF: Structural and functional characterization of potent antithrombotic oligonucleotides possessing both quadruplex and duplex motifs. Biochemistry 1995, 34:4478-4492.
11. Tsiang M, Gibbs CS, Griffin LC, Dunn KE, Leung LK: Selection of a supressor mutation that restores affinity of an oligonucleotide inhibitor for thrombin using in vitro genetics. J Biol Chem 1995, 270:19370-19376.
12. Lin Y, Padmapriya A, Morden KM, Jayasena SD: Peptide conjugation to an in vitro-selected DNA ligand improves enzyme inhibition. Proc Natl Acad Sci USA 1995, 92:11044-11048. A DNA aptamer for neutrophil elastase is linked to an inhibitory tetrapeptide to create a chimeric DNA-protein that has greater binding affinity and inhibitory function than either of the individual components.
13. i of 0.3 nM.
14. Hale SP, Schimmel P: Protein synthesis editing by a DNA aptamer. Proc Natl Acad Sci USA 1996, 93:2755-2758. In most cases, aptamers for specific enzyme targets are made with the intent to inhibit catalytic function. This DNA aptamer binds to isoleucyl-tRNA synthetase and induces an enzymatic activity that reduces the frequency of tRNA mischarging.
15. Huizenga DE, Szostak JW: A DNA aptamer that binds adenosine and ATP. Biochemistry 1995, 34:656-665. An excellent demonstration of the binding specificity and affinity of a DNA aptamer that functions as a receptor for adenosine and its 5′-phosphorylated derivatives. This DNA aptamer and a previously reported RNA aptamer for the same ligand have nearly identical functional characteristics, but the two receptors have entirely different structures. This finding supports the notion that RNAs and DNAs may need to use very different structural motifs to perform identical tasks.
16. Sassanfar M, Szostak JW: An RNA motif that binds ATP. Nature 1993, 364:550-553.
17. Li Y, Geyer CR, Sen D: Recognition of anionic porphyrins by DNA aptamers. Biochemistry 1996, 35:6911-6922.
18. Harada K, Frankel AD: Identification of two novel arginine binding DNAs. EMBO J 1995, 23:5798-5811. This paper reports the isolation and characterization of two classes of arginine-binding DNAs. One class may use atypical tetra-base interactions to form a structure that is similar to stacked G-quarlets.
19. Mishra R, Tinevez R, Toulme J-J: Targeting nucleic acid secondary structures by antisense oligonucleotides designed through in vitro selection. Proc Natl Acad Sci USA 1996, 93:10679-10684.
20. Cate JH, Goodling AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA: Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 1996, 273:1678-1684.
21. 2+-dependent DNA enzymes remain active under conditions that simulate the temperature and ionic strength conditions of mammalian cells.
22. Breaker RR, Joyce GF: A DNA enzyme that cleaves RNA. Chem Biol 1994, 1:223-229.
23. Cuenoud B, Szostak JW: A DNA metalloenzyme with DNA ligase activity. Nature 1995, 375:611-614. This report describes the selection and characterization of a DNA enzyme that catalyzes the ligation of DNAs with a rate enhancement of -3 400-fold over the rate observed using simple DNA template mediated catalysis. This finding suggests that certain catalytic DNAs may be capable of promoting the template-directed synthesis of new DNA.
24. 6-fold.
25. Li Y, Sen D: A catalytic DNA for porphyrin metallation. Nat Struct Biol 1996, 3:743-747. This is the first example of indirect selection of a catalytic DNA. The authors have individually screened DNA aptamers that bind N-methylmesoporphyrin IX (NMM, a transition-state analogue for porphyrin metalation) for the ability to catalyze the metalation of mesoporphyrin IX. This approach, which is similar to that used to create catalytic antibodies, takes advantage of the probability that some DNAs that can bind NMM might also stabilize the transition state for mesoporphyrin IX metalation, and thereby catalyze this reaction.
26. Conn MM, Prudent JR, Schultz PG: Porphyrin metalation catalyzed by a small RNA molecule. J Am Chem Soc 1996, 118:7012-7013.
27. Wyatt JR, Vickers TA, Roberson JL, Buckheit RW Jr, Klimkait T, DeBaets E, Rayner B, Imbach JL, Ecker DJ: Combinatorially selected guanosine-quartet structure is a potent inhibitor of human immunodeficiency virus envelope-mediated fusion. Proc Natl Acad Sci USA 1994, 91:1356-1360.