Mutational analysis of a signaling aptamer suggests a mechanism for ligand-triggered structure-switching

Biochemical and Biophysical Research Communications

Volumn 378, Issue 1, 2009, Pages 51-56

  Vandenengel, Jeffrey E ^a   Morse, Daniel P ^a  

^a UNITED STATES NAVAL ACADEMY   (United States)

Author keywords

Aptamer; In vitro selection; Mechanism; Mutagenesis; RNA; Structure switching

Indexed keywords

APTAMER; LIGAND; TOBRAMYCIN;

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; GENE REARRANGEMENT; MUTATIONAL ANALYSIS; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; STRUCTURE ANALYSIS;

ANTI-BACTERIAL AGENTS; APTAMERS, NUCLEOTIDE; BINDING SITES; DNA MUTATIONAL ANALYSIS; FLUORESCENCE; LIGANDS; NUCLEIC ACID CONFORMATION; RNA; STRUCTURE-ACTIVITY RELATIONSHIP; TOBRAMYCIN;

EID: 56949088663     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2008.10.180     Document Type: Article

References (18)

1. Nutiu R., and Li Y. Structure-switching signaling aptamers: transducing molecular recognition into fluorescence signaling. Chemistry 10 (2004) 1868-1876
2. Edwards T.E., Klein D.J., and Ferre-D'Amare A.R. Riboswitches: small-molecule recognition by gene regulatory RNAs. Curr. Opin. Struct. Biol. 17 (2007) 273-279
3. Montange R.K., and Batey R.T. Riboswitches: emerging themes in RNA structure and function. Annu. Rev. Biophys. 37 (2008) 117-133
4. Wakeman C.A., Winkler W.C., and Dann III C.E. Structural features of metabolite-sensing riboswitches. Trends Biochem. Sci. 32 (2007) 415-424
5. Suess B., and Weigand J.E. Engineered riboswitches: overview, problems and trends. RNA Biol. 5 (2008) 24-29
6. Morse D.P. Direct selection of RNA beacon aptamers. Biochem. Biophys. Res. Commun. 359 (2007) 94-101
7. Nutiu R., and Li Y. In vitro selection of structure-switching signaling aptamers. Angew. Chem. Int. Ed. Engl. 44 (2005) 1061-1065
8. Rajendran M., and Ellington A.D. Selection of fluorescent aptamer beacons that light up in the presence of zinc. Anal. Bioanal. Chem. 390 (2008) 1067-1075
9. Walter A.E., Turner D.H., Kim J., Lyttle M.H., Muller P., Mathews D.H., and Zuker M. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl. Acad. Sci. USA 91 (1994) 9218-9222
10. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415
11. Woese C.R., Magrum L.J., Gupta R., Siegel R.B., Stahl D.A., Kop J., Crawford N., Brosius J., Gutell R., Hogan J.J., and Noller H.F. Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Nucleic Acids Res. 8 (1980) 2275-2293
12. Gutell R.R., Noller H.F., and Woese C.R. Higher order structure in ribosomal RNA. EMBO J. 5 (1986) 1111-1113
13. Gutell R.R., Lee J.C., and Cannone J.J. The accuracy of ribosomal RNA comparative structure models. Curr. Opin. Struct. Biol. 12 (2002) 301-310
14. Engelen S., and Tahi F. Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences. BMC Bioinformatics 8 (2007) 464
15. Jiang L., Suri A.K., Fiala R., and Patel D.J. Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex. Chem. Biol. 4 (1997) 35-50
16. Jiang L., and Patel D.J. Solution structure of the tobramycin-RNA aptamer complex. Nat. Struct. Biol. 5 (1998) 769-774
17. Verhelst S.H., Michiels P.J., van der Marel G.A., van Boeckel C.A., and van Boom J.H. Surface plasmon resonance evaluation of various aminoglycoside-RNA hairpin interactions reveals low degree of selectivity. Chembiochem 5 (2004) 937-942
18. Ryu D.H., and Rando R.R. Aminoglycoside binding to human and bacterial A-Site rRNA decoding region constructs. Bioorg. Med. Chem. 9 (2001) 2601-2608