Selection and evolution of NTP-specific aptamers

Nucleic Acids Research

Volumn 32, Issue 17, 2004, Pages 5045-5058

  Weill, Laure ^a   Louis, Dominique ^a,b   Sargueil, Bruno ^a  

^a CNRS   (France)

^b Evologic SA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE DERIVATIVE; ADENOSINE TRIPHOSPHATE; APTAMER; CORDYCEPIN; RNA; SUGAR PHOSPHATE; DEOXYADENOSINE DERIVATIVE; DRUG DERIVATIVE; MAGNESIUM CHLORIDE; NUCLEOTIDE; OLIGORIBONUCLEOTIDE; SEPHAROSE; SODIUM CHLORIDE;

ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; IN VITRO STUDY; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN MOTIF; RNA ANALYSIS; RNA BINDING; RNA ISOLATION; RNA SEQUENCE; RNA STRUCTURE; STRUCTURE ANALYSIS; BINDING SITE; CHEMISTRY; CLASSIFICATION; CONFORMATION; DIRECTED MOLECULAR EVOLUTION; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT;

ADENOSINE TRIPHOSPHATE; BASE SEQUENCE; BINDING SITES; DEOXYADENOSINES; DIRECTED MOLECULAR EVOLUTION; MAGNESIUM CHLORIDE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; OLIGORIBONUCLEOTIDES; PHYLOGENY; SEPHAROSE; SEQUENCE ALIGNMENT; SODIUM CHLORIDE;

EID: 4844227634     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh835     Document Type: Article

References (53)

1. Famulok,M. (1999) Oligonucleotide aptamers that recognize small molecules. Curr. Opin. Struct. Biol., 9, 324-329.
2. Gold,L., Polisky,B., Uhlenbeck,O. and Yarus,M. (1995) Diversity of oligonucleotide functions. Annu. Rev. Biochem., 64 763-797.
3. Jayasena,S.D. (1999) Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem., 45, 1628-1650.
4. Brody,E.N. and Gold,L. (2000) Aptamers as therapeutic and diagnostic agents. J. Biotechnol., 74, 5-13.
5. Burgstaller,P., Jenne,A. and Blind,M. (2002) Aptamers and aptazymes: accelerating small molecule drug discovery. Curr. Opin. Drug Discov. Devel., 5, 690-700.
6. Hermann,T. and Patel,D.J. (2000) Adaptive recognition by nucleic acid aptamers. Science, 287, 820-825.
7. Feigon,J., Dieckmann,T. and Smith,F.W. (1996) Aptamer structures from A to zeta. Chem. Biol., 3, 611-617.
8. Patel,D.J. and Suri,A.K. (2000) Structure, recognition and discrimination in RNA aptamer complexes with cofactors, amino acids, drugs and aminoglycoside antibiotics. J. Biotechnol., 74, 39-60.
9. Yang,Y., Kochoyan,M., Burgstaller,P., Westhof,E. and Famulok,M. (1996) Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science, 272 1343-1347.
10. Bartel,D.P. and Unrau,P.J. (1999) Constructing an RNA world. Trends Cell Biol., 9, M9-M13.
11. Lorsch,JR. and Szostak,J.W. (1994) In vitro evolution of new ribozymes with polynucleotide kinase activity. Nature, 371, 31-36.
12. Wilson,C. and Szostak,J.W. (1995) In vitro evolution of a self-alkylating ribozyme. Nature, 374, 777-782.
13. Burke,D.H. and Hoffman,D.C. (1998) A novel acidophilic RNA motif that recognizes coenzyme A. Biochemistry, 37, 4653-4663.
14. Burke,D.H. and Gold,L. (1997) RNA aptamers to the adenosine moiety of S-adenosyl methionine: structural inferences from variations on a theme and the reproducibility of SELEX. Nucleic Acids Res., 25 2020-2024.
15. Huizenga,D.E. and Szostak,J.W. (1995) A DNA aptamer that binds adenosine and ATP. Biochemistry, 34, 656-665.
16. Koizumi,M. and Breaker,R.R. (2000) Molecular recognition of cAMP by an RNA aptamer. Biochemistry, 39, 8983-8992.
17. Huang,Z. and Szostak,J.W. (2003) Evolution of aptamers with a new specificity and new secondary structures from an ATP aptamer. RNA 9, 1456-1463.
18. Sassanfar,M. and Szostak,J.W. (1993) An RNA motif that binds ATP. Nature, 364, 550-553.
19. Meli,M., Vergne,J., Decout,J.L. and Maurel,M.C. (2002) Adenine-aptamer complexes: a bipartite RNA site that binds the adenine nucleic base. J. Biol. Chem., 277, 2104-2111.
20. Davis,J.H. and Szostak,J.W. (2002) Isolation of high-affinity GTP aptamers from partially structured RNA libraries. Proc. Natl Acad. Sci. USA, 99, 11616-11621.
21. Kiga,D., Futamura,Y., Sakamoto,K. and Yokoyama,S. (1998) An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition. Nucleic Acids Res., 26, 1755-1760.
22. Gebhardt,K., Shokraei,A., Babaie,E. and Lindqvist,B.H. (2000) RNA aptamers to S-adenosylhomocysteine: kinetic properties, divalent cation dependency, and comparison with anti-S adenosylhomocysteine antibody. Biochemistry, 39, 7255-7265.
23. Lauhon,C.T. and Szostak,J.W. (1995) RNA aptamers that bind flavin and nicotinamide redox cofactors. J. Am. Chem. Soc., 117 1246-1257.
24. Dieckmann,T., Butcher,S.E., Sassanfar,M., Szostak,J.W. and Feigon,J. (1997) Mutant ATP-binding RNA aptamers reveal the structural basis for ligand binding. J. Mol. Biol., 273, 467-478.
25. Dieckmann,T., Suzuki,E., Nakamura,G.K. and Feigon,J. (1996) Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA, 2, 628-640.
26. Jiang,F., Kumar,R.A., Jones,R.A. and Patel,D.J. (1996) Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature, 382, 183-186.
27. Burgstaller,P. and Famulok,M. (1994) Isolation of RNA-aptamers for biological cofactors by in vitro selection. Angew. Chem., 106, 1163-1166.
28. Shu,D. and Guo,P. (2003) A viral RNA that binds ATP and contains a motif similar to an ATP-binding aptamer from SELEX. J. Biol. Chem., 278, 7119-7125.
29. Unrau,P.J. and Bartel,D.P. (1998) RNA-catalysed nucleotide synthesis. Nature, 395, 260-263.
30. Huang,F., Yang,Z. and Yarus,M. (1998) RNA enzymes with two small-molecule substrates. Chem. Biol., 5, 669-678.
31. Huang,F. and Yarus,M. (1997) 5′-RNA self-capping from guanosine diphosphate. Biochemistry, 36, 6557-6563.
32. Illangasekare,M., Sanchez,G., Nickles,T. and Yarus,M. (1995) Aminoacyl-RNA synthesis catalyzed by an RNA. Science, 267, 643-647.
33. Tsukiji,S., Pattnaik,S.B. and Suga,H. (2003) An alcohol dehydrogenase ribozyme. Nature Struct. Biol., 10, 713-717.
34. Chapman,K.B. and Szostak,J.W. (1995) Isolation of a ribozyme with 5′-5′ ligase activity. Chem. Biol., 2, 325-333.
35. Bartel,D.P. and Szostak,J.W. (1993) Isolation of new ribozymes from a large pool of random sequences [see comment]. Science 261, 1411-1418.
36. Lohse,P.A. and Szostak,J.W. (1996) Ribozyme-catalysed amino-acid transfer reactions. Nature, 381, 442-444.
37. Santoro,S.W. and Joyce,G.F. (1997) A general purpose RNA-cleaving DNA enzyme. Proc. Natl Acad. Sci. USA, 94, 4262-4266.
38. Geiger,A., Burgstaller,P., von der Eltz,H., Roeder,A. and Famulok,M. (1996) RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity. Nucleic Acids Res. 24, 1029-1036.
39. Milligan,J.F. and Uhlenbeck,O.C. (1989) Synthesis of small RNAs using T7 RNA polymerase. Meth. Enzymol., 180, 51-62.
40. Vartanian,J.P., Henry,M. and Wain-Hobson,S. (1996) Hypermutagenic PCR involving all four transitions and a sizeable proportion of transversions. Nucleic Acids Res., 24, 2627-2631.
41. Butcher,S.E. and Burke,J.M. (1994) Structure-mapping of the hairpin ribozyme. Magnesium-dependent folding and evidence for tertiary interactions within the ribozyme-substrate complex. J. Mol. Biol., 244, 52-63.
42. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
43. Sabeti,P.C., Unrau,P.J. and Bartel,D.P. (1997) Accessing rare activities from random RNA sequences: the importance of the length of molecules in the starting pool. Chem. Biol., 4, 767-774.
44. Jenison,R.D., Gill,S.C., Pardi,A. and Polisky,B. (1994) High-resolution molecular discrimination by RNA. Science, 263 1425-1429.
45. Egli,M., Minasov,G., Su,L. and Rich,A. (2002) Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution. Proc. Natl Acad. Sci. USA, 99, 4302-4307.
46. Gonzalez,R.L.,Jr and Tinoco,I.,Jr (1999) Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudoknot. J. Mol. Biol., 289, 1267-1282.
47. Nixon,P.L. and Giedroc,D.P. (1998) Equilibrium unfolding (folding) pathway of a model H-type pseudoknotted RNA: the role of magnesium ions in stability. Biochemistry, 37, 16116-16129.
48. Eckstein,F. (2002) Developments in RNA chemistry, a personal view. Biochimie, 84, 841-848.
49. Been,M.D. and Perrotta,A.T. (1991) Group I intron self-splicing with adenosine: evidence for a single nucleoside-binding site. Science, 252, 434-437.
50. Michel,F., Hanna,M., Green,R., Bartel,D.P. and Szostak,J.W. (1989) The guanosine binding site of the Tetrahymena ribozyme. Nature 342, 391-395.
51. Saenger,W. (1984) Principles of Nucleic Acid Structure. Springer-Verlag, NY.
52. Westhof,E., Plach,H., Cuno,I. and Ludemann,H.D. (1977) Proton magnetic resonance studies of 2′-,3′-, and 5′ -deoxyadenosine conformations in solution. Nucleic Acids Res., 4, 939-953.
53. Guschlbauer,W. and Jankowski,K. (1980) Nucleoside conformation is determined by the electronegativity of the sugar substituent. Nucleic Acids Res., 8, 1421-1433.