1997
DOI: 10.1021/ja964290o
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Direct Observation of Aminoglycoside−RNA Interactions by Surface Plasmon Resonance

Abstract: The specificity of neomycin B and related aminoglycoside antibiotics in their interaction with the Rev responsive element (RRE) of HIV-1 mRNA has been studied by directly observing the aminoglycoside-RNA complexes using surface plasmon resonance. Several different RNA sequences, each with a biotin tag, have been prepared using T7 RNA polymerase-catalyzed transcription of synthetic DNA templates and have been immobilized on a streptavidin-coated surface for the binding study. The results indicate that neomycin … Show more

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Cited by 201 publications
(153 citation statements)
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“…Proper interpretation of the data from assays for RNAligand interactions such as ITC (Gilbert and Batey 2009), fluorescence quenching (Davies and Arenz 2008), fluorescence anisotropy (Luedtke et al 2003), or surface plasmon resonance (Hendrix et al 1997) require the accurate determination of parameters that include the concentration of the RNA. In this study, we show that application of Beer's law using the algorithms currently utilized by online calculators (http://www.idtdna.com/Analyzer/Applications/Instructions/ Default.aspx?AnalyzerDefinitions=true) result in an underestimation of sample concentrations due to the hypochromic effect for structured RNAs like riboswitches (Table 1).…”
Section: Resultsmentioning
confidence: 99%
“…Proper interpretation of the data from assays for RNAligand interactions such as ITC (Gilbert and Batey 2009), fluorescence quenching (Davies and Arenz 2008), fluorescence anisotropy (Luedtke et al 2003), or surface plasmon resonance (Hendrix et al 1997) require the accurate determination of parameters that include the concentration of the RNA. In this study, we show that application of Beer's law using the algorithms currently utilized by online calculators (http://www.idtdna.com/Analyzer/Applications/Instructions/ Default.aspx?AnalyzerDefinitions=true) result in an underestimation of sample concentrations due to the hypochromic effect for structured RNAs like riboswitches (Table 1).…”
Section: Resultsmentioning
confidence: 99%
“…Our structural understanding of speci®c aminoglycoside binding to RNA has recently progressed following publication of two NMR structures of aminoglycoside/RNA complexes (Jiang et al, 1996;Fourmy et al, 1996) and the results obtained by applying various techniques to study aminoglycoside/RNA interaction (Wang & Rando, 1995;Wallis et al, 1995;Werstuck et al, 1996;Famulok & Hu È ttenhofer, 1996;Hendrix et al, 1997;Wang & Tor, 1997a,b). Biochemical data suggest that the inhibitory effect of neomycin on the hammerhead ribozyme is based on competitive binding to the RNA between the polycationic aminoglycoside and the Mg 2 (Clouet-d'Orval et al, 1995), which are required for both folding and catalysis (Dahm & Uhlenbeck, 1991;Long et al, 1995).…”
Section: Introductionmentioning
confidence: 99%
“…Circular dichroism can distinguish between RNA groove binding and intercalation but cannot identify individual binding sites (15). Other techniques that are valuable for determining noncovalent binding of small molecules to RNA, such as mass spectrometry (16), fluorescence (17), and surface plasmon resonance (18,19), yield binding constants but do not give structural information.…”
mentioning
confidence: 99%