Codeine-binding RNA aptamers and rapid determination of their binding constants using a direct coupling surface plasmon resonance assay

Nucleic Acids Research

Volumn 34, Issue 19, 2006, Pages 5670-5682

  Win, Maung Nyan ^a   Klein, Joshua S ^a   Smolke, Christina D ^a  

^a California Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; BENZYLISOQUINOLINE DERIVATIVE; CARRIER PROTEIN; CODEINE; MORPHINE; RNA; THEBAINE;

ACCURACY; ARTICLE; BINDING AFFINITY; BIOASSAY; CONTROLLED STUDY; DRUG RECEPTOR BINDING; DRUG STRUCTURE; EQUILIBRIUM CONSTANT; HIGH THROUGHPUT SCREENING; KINETICS; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA BINDING; RNA SEQUENCE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; SURFACE PLASMON RESONANCE;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; BENZYLISOQUINOLINES; BINDING SITES; CODEINE; CONSERVED SEQUENCE; KINETICS; MOLECULAR SEQUENCE DATA; NARCOTICS; NUCLEIC ACID CONFORMATION; SELEX APTAMER TECHNIQUE; SEQUENCE ANALYSIS, RNA; SURFACE PLASMON RESONANCE;

EID: 33750968498     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl718     Document Type: Article

References (39)

1. William,D.G., Hatch,D.J. and Howard,R.F. (2001) Codeine phosphate in paediatric medicine. Br. J. Anaesth., 86, 413-421.
2. Williams,D.G., Patel,A. and Howard,R.F. (2002) Pharmacogenetics of codeine metabolism in an urban population of children and its implications for analgesic reliability. Br. J. Anaesth., 89, 839-845.
3. Kim,I., Barnes,A.J., Oyler,J.M., Schepers,R., Joseph,R.E., Jr, Cone,E.J., Lafko,D., Moolchan,E.T. and Huestis,M.A. (2002) Plasma and oral fluid pharmacokinetics and pharmacodynamics after oral codeine administration. Clin. Chem., 48, 1486-1496.
4. Jayasena,S.D. (1999) Aptamers: An emerging class of molecules that rival antibodies in diagnostics. Clin. Chem., 45, 1628-1650.
5. Silverman,S.K. (2003) Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA RNA, 9, 377-383.
6. O'Sullivan,C.K. (2002) Aptasensors - the future of biosensing? Anal. Bioanal. Chem., 372, 44-48.
7. Hesselberth,J.R., Robertson,M.P., Knudsen,S.M. and Ellington,A.D. (2003) Simultaneous detection of diverse analytes with an aptazyme ligase array. Anal. Biochem., 312, 106-112.
8. Seetharaman,S., Zivarts,M., Sudarsan,N. and Breaker,R.R. (2001) Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nat. Biotechnol., 19, 336-341.
9. Facchini,P.J. (2001) Alkaloid biosynthesis in plants: Biochemistry, Cell Biology, Molecular Regulation, and Metabolic Engineering Applications. Annu. Rev. Plant Physiol. Plant Mol. Biol., 52, 29-66.
10. Allen,R.S., Millgate,A.G., Chitty,J.A., Thisleton,J., Miller,J.A., Fist,A.J., Gerlach,W.L. and Larkin,P.J. (2004) RNAi-mediated replacement of morphine with the nonnarcotic alkaloid reticuline in opium poppy. Nat. Biotechnol., 22, 1559-1566.
11. Rathbone,D.A. and Bruce,N.C. (2002) Microbial transformation of alkaloids. Curr. Opin. Microbiol., 5, 274-281.
12. Suess,B., Hanson,S., Berens,C., Fink,B., Schroeder,R. and Hillen,W. (2003) Conditional gene expression by controlling translation with tetracycline-binding aptamers. Nucleic Acids Res., 31, 1853-1858.
13. Suess,B., Fink,B., Berens,C., Stentz,R. and Hillen,W. (2004) A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res., 32, 1610-1614.
14. Werstuck,G. and Green,M.R. (1998) Controlling gene expression in living cells through small molecule-RNA interactions. Science, 282, 296-298.
15. Desai,S.K. and Gallivan,J.P. (2004) Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J. Am. Chem. Soc., 126, 13247-13254.
16. Winkler,W.C. and Breaker,R.R. (2005) Regulation of bacterial gene expression by riboswitches. Annu. Rev. Microbiol., 59, 487-517.
17. Bayer,T.S. and Smolke,C.D. (2005) Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol., 23, 337-343.
18. Mannironi,C., Di Nardo,A., Fruscoloni,P. and Tocchini-Valentini,G.P. (1997) In vitro selection of dopamine RNA ligands. Biochemistry, 36, 9726-9734.
19. Mannironi,C., Scerch,C., Fruscoloni,P. and Tocchini-Valentini,G.P. (2000) Molecular recognition of amino acids by RNA aptamers: The evolution into an L-tyrosine binder of a dopamine-binding RNA motif. RNA, 6, 520-527.
20. Tuerk,C. and Gold,L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
21. Ellington,A.D. and Szostak,J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818-822.
22. Kwon,M., Chun,S.M., Jeong,S. and Yu,J. (2001) In vitro selection of RNA against kanamycin B. Mol. Cells, 11, 303-311.
23. 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.
24. Jeong,S., Eom,T., Kim,S., Lee,S. and Yu,J. (2001) In vitro selection of the RNA aptamer against the Sialyl Lewis X and its inhibition of the cell adhesion. Biochem. Biophys. Res. Commun., 281, 237-243.
25. Verhelst,S.H., Michiels,P.J., van der Marel,G.A., van Boeckel,C.A. and van Boom,J.H. (2004) Surface plasmon resonance evaluation of various aminoglycoside-RNA hairpin interactions reveals low degree of selectivity. Chembiochem, 5, 937-942.
26. 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.
27. Arnold,F.H. and Blanch,H.W. (1986) Analytical affinity chromatography II. Rate theory and the measurement of biological binding kinetics. J. Chromatogr., 355, 13-27.
28. Brockstedt,U., Uzarowska,A., Montpetit,A., Pfau,W. and Labuda,D. (2004) In vitro evolution of RNA aptamers recognizing carcinogenic aromatic amines. Biochem. Biophys. Res. Commun., 313, 1004-1008.
29. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
30. Berens,C., Thain,A. and Schroeder,R. (2001) A tetracycline-binding RNA aptamer. Bioorg. Med. Chem., 9, 2549-2556.
31. Lozupone,C., Changayil,S., Majerfeld,I. and Yarus,M. (2003) Selection of the simplest RNA that binds isoleucine. RNA, 9, 1315-1322.
32. Majerfeld,I. and Yarus,M. (1998) Isoleucine:RNA sites with associated coding sequences. RNA, 4, 471-478.
33. Jenison,R.D., Gill,S.C., Pardi,A. and Polisky,B. (1994) High-resolution molecular discrimination by RNA. Science, 263, 1425-1429.
34. Haller,A.A. and Sarnow,P. (1997) In vitro selection of a 7-methyl-guanosine binding RNA that inhibits translation of capped mRNA molecules. Proc. Natl Acad. Sci. USA, 94, 8521-8526.
35. Myszka,D.G. and Morton,T.A. (1998) CLAMP: A biosensor kinetic data analysis program. Trends Biochem. Sci., 23, 149-150.
36. Wang,Y. and Rando,R.R. (1995) Specific binding of aminoglycoside antibiotics to RNA. Chem. Biol., 2, 281-290.
37. Wang,Y., Killian,J., Hamasaki,K. and Rando,R.R. (1996) RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities. Biochemistry, 35, 12338-12346.
38. Hamasaki,K., Killian,J., Cho,J. and Rando,R.R. (1998) Minimal RNA constructs that specifically bind aminoglycoside antibiotics with high affinities. Biochemistry, 37, 656-663.
39. Cho,J., Hamasaki,K. and Rando,R.R. (1998) The binding site of a specific aminoglycoside binding RNA molecule. Biochemistry, 37, 4985-4992.