One RNA aptamer sequence, two structures: A collaborating pair that inhibits AMPA receptors

Nucleic Acids Research

Volumn 37, Issue 12, 2009, Pages 4022-4032

  Huang, Zhen ^a   Pei, Weimin ^a   Han, Yan ^a   Jayaseelan, Sabarinath ^a   Shekhtman, Alexander ^a   Shi, Hua ^a   Niu, Li ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPA RECEPTOR; APTAMER; GLUTAMATE RECEPTOR 2; RNA;

ARTICLE; COMBINATORIAL CHEMISTRY; CONTROLLED STUDY; ENZYME INHIBITION; GENE DUPLICATION; HUMAN; HUMAN CELL; MOLECULE; NUCLEOTIDE BINDING SITE; PHENOTYPE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; RNA SEQUENCE; RNA TRANSCRIPTION;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; CELL LINE; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RECEPTORS, AMPA; RNA; SELEX APTAMER TECHNIQUE; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION, GENETIC;

EID: 67651166851     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp284     Document Type: Article

References (38)

1. Huynen,M.A., Stadler,P.F. and Fontana,W. (1996) Smoothness within ruggedness: The role of neutrality in adaptation. Proc. Natl Acad. Sci. USA, 93, 397-401.
2. Schultes,E.A. and Bartel,D.P. (2000) One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science, 289, 448-452.
3. Mandal,M. and Breaker,R.R. (2004) Gene regulation by riboswitches. Nat. Rev. Mol. Cell Biol., 5, 451-463.
4. Tuerk,C. and Gold,L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
5. Ellington,A.D. and Szostak,J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818-822.
6. Huang,Z., Pei,W., Jayaseelan,S., Shi,H. and Niu,L. (2007) RNA aptamers selected against the GluR2 glutamate receptor channel. Biochemistry 46, 12648-12655.
7. Hollmann,M. and Heinemann,S. (1994) Cloned glutamate receptors. Annu. Rev. Neurosci., 17, 31-108.
8. Dingledine,R., Borges,K., Bowie,D. and Traynelis,S.F. (1999) The glutamate receptor ion channels. Pharmacol. Rev., 51, 7-61.
9. Batey,R.T. and Kieft,J.S. (2007) Improved native affinity purification of RNA. RNA, 13, 1384-1389. Epub 2007 Jun 1384.
10. Winkler,W.C., Nahvi,A., Roth,A., Collins,J.A. and Breaker,R.R. (2004) Control of gene expression by a natural metabolite-responsive ribozyme. Nature, 428, 281-286.
11. McMaster,G.K. and Carmichael,G.G. (1977) Analysis of single-and double-stranded nucleic acids on polyacrylamide and agarose gels by using glyoxal and acridine orange. Proc. Natl Acad. Sci. USA., 74, 4835-4838.
12. Sambrook,J. and Rusell,D.W. (2001) Molecular Cloning, A Laboratory Manual, 3rd edn. Cold Spring Harbor Laboratory Press, New York, pp. 7.27-7.30.
13. Wilkinson,K.A., Merino,E.J. and Weeks,K.M. (2005) RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts. J. Am. Chem. Soc., 127 4659-4667.
14. Li,G., Pei,W. and Niu,L. (2003) Channel-opening kinetics of GluR2Q(flip) AMPA receptor: A laser-pulse photolysis study. Biochemistry, 42 12358-12366.
15. Li,G., Oswald,R.E. and Niu,L. (2003) Channel-opening kinetics of GluR6 kainate receptor. Biochemistry, 42, 12367-12375.
16. Honore,T., Davies,S.N., Drejer,J., Fletcher,E.J., Jacobsen,P., Lodge,D. and Nielsen,F.E. (1988) Quinoxalinediones: Potent competitive non-NMDA glutamate receptor antagonists. Science, 241, 701-703.
17. Harrison,G.P., Mayo,M.S., Hunter,E. and Lever,A.M. (1998) Pausing of reverse transcriptase on retroviral RNA templates is in.uenced by secondary structures both 5′ and 3′ of the catalytic site. Nucleic Acids Res., 26, 3433-3442.
18. Klasens,B.I., Huthoff,H.T., Das,A.T., Jeeninga,R.E. and Berkhout,B. (1999) The effect of template RNA structure on elongation by HIV-1 reverse transcriptase. Biochim. Biophys Acta., 1444, 355-370.
19. Soukup,G.A. and Breaker,R.R. (1999) Relationship between internucleotide linkage geometry and the stability of RNA. RNA, 5, 1308-1325.
20. Celander,D.W. and Cech,T.R. (1991) Visualizing the higher order folding of a catalytic RNA molecule. Science, 251, 401-407.
21. Cate,J.H. and Doudna,J.A. (1996) Metal-binding sites in the major groove of a large ribozyme domain. Structure, 4, 1221-1229.
22. Usher,D.A. and McHale,A.H. (1976) Hydrolytic stability of helical RNA: A selective advantage for the natural 3′,5′-bond. Proc. Natl Acad. Sci. USA, 73, 1149-1153.
23. Jin,R., Chapman,W.H. Jr, Srinivasan,A.R., Olson,W.K., Breslow,R. and Breslauer,K.J. (1993) Comparative spectroscopic, calorimetric, and computational studies of nucleic acid complexes with 2′,5′-versus 3′,5′-phosphodiester linkages. Proc. Natl Acad. Sci. USA, 90, 10568-10572.
24. Puglisi,E.V., Puglisi,J.D., Williamson,J.R. and RajBhandary,U.L. (1994) NMR analysis of tRNA acceptor stem microhelices: Discriminator base change affects tRNA conformation at the 3′ end. Proc. Natl Acad. Sci. USA, 91, 11467-11471.
25. Wilkinson,K.A., Gorelick,R.J., Vasa,S.M., Guex,N., Rein,A., Mathews,D.H., Giddings,M.C. and Weeks,K.M. (2008) High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol., 6, e96.
26. Mathews,D.H., Disney,M.D., Childs,J.L., Schroeder,S.J., Zuker,M. and Turner,D.H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl Acad. Sci. USA, 101, 7287-7292.
27. Mortimer,S.A. and Weeks,K.M. (2007) A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J. Am. Chem. Soc., 129, 4144-4145.
28. Doty,P., Boedtker,H., Fresco,J.R., Haselkorn,R. and Litt,M. (1959) Secondary Structure in Ribonucleic Acids. Proc. Natl Acad. Sci. USA 45, 482-499.
29. Roth,A., Nahvi,A., Lee,M., Jona,I. and Breaker,R.R. (2006) Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions. RNA, 12, 607-619.
30. Herschlag,D. (1995) RNA chaperones and the RNA folding problem. J. Biol. Chem., 270, 20871-20874.
31. Khvorova,A., Lescoute,A., Westhof,E. and Jayasena,S.D. (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat. Struct. Biol., 10, 708-712.
32. Schroeder,R., Barta,A. and Semrad,K. (2004), Nat. Rev. Mol. Cell Biol., 5, pp. 908-919.
33. Lewicki,B.T., Margus,T., Remme,J. and Nierhaus,K.H. (1993) Coupling of rRNA transcription and ribosomal assembly in vivo. Formation of active ribosomal subunits in Escherichia coli requires transcription of rRNA genes by host RNA polymerase which cannot be replaced by bacteriophage T7 RNA polymerase. J. Mol. Biol., 231, 581-593.
34. Pan,T., Fang,X. and Sosnick,T. (1999) Pathway modulation, circular permutation and rapid RNA folding under kinetic control. J. Mol. Biol., 286, 721-731.
35. Spiegelman,S. (1971) An approach to the experimental analysis of precellular evolution. Q. Rev. Biophys., 4, 213-253.
36. Bornberg-Bauer,E. (1997) How are model protein structures distributed in sequence space? Biophys. J., 73, 2393-2403.
37. Paul,N., Springsteen,G. and Joyce,G.F. (2006) Conversion of a ribozyme to a deoxyribozyme through in vitro evolution. Chem. Biol., 13 329-338.
38. Das,R., Laederach,A., Pearlman,S.M., Herschlag,D. and Altman,R.B. (2005) SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA, 11, 344-354.