RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities

Yong Wang, Jennifer Killian, Keita Hamasaki, Robert R. Rando

Research output: Contribution to journalArticle

114 Citations (Scopus)

Abstract

RNA aptamers had previously been selected which were able to bind to the aminoglycoside antibiotic tobramycin with high affinity (Wang and Rando, 1995). Consensus sequences are found in a variety of constructs, and these sequences were mapped to stem-loop regions by Mfold secondary structure prediction. A tobramycin-based affinity cleavage reagent specifically cleaves the aptamers in their consensus regions. A fluorescence depolarization method is developed to accurately measure the affinity and stoichiometry of aminoglycoside binding to RNA constructs. An RNA aptamer (J6RNA) selected to bind to the aminoglycoside antibiotic tobramycin is shown to do so with an affinity of 0.77 nM and a stoichiometry of 1:1. (Fluorescently labeled) 5- carboxytetramethylrhodamine tobramycin (CRT) is used as a ligand in the fluorescence depolarization studies. J6RNA binding is quite specific for tobramycin, and weakly binds structurally related aminoglycosides with affinities 103-104 -fold lower than that for tobramycin. Specific aminoglycoside binding aptamers of this type should be useful for revealing the rules of RNA-aminoglycoside recognition.

Original languageEnglish
Pages (from-to)12338-12346
Number of pages9
JournalBiochemistry
Volume35
Issue number38
DOIs
Publication statusPublished - 1996
Externally publishedYes

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Tobramycin
Aminoglycosides
RNA
Anti-Bacterial Agents
Molecules
Nucleotide Aptamers
Depolarization
Stoichiometry
Fluorescence
Ligands

ASJC Scopus subject areas

  • Biochemistry

Cite this

RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities. / Wang, Yong; Killian, Jennifer; Hamasaki, Keita; Rando, Robert R.

In: Biochemistry, Vol. 35, No. 38, 1996, p. 12338-12346.

Research output: Contribution to journalArticle

Wang, Yong ; Killian, Jennifer ; Hamasaki, Keita ; Rando, Robert R. / RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities. In: Biochemistry. 1996 ; Vol. 35, No. 38. pp. 12338-12346.
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