Ethidium bromide binding to transfer RNA: transfer RNA as a model system for studying drug-RNA interactions

Jones, Claude R.; Bolton, Philip H.; Kearns, David R.

doi:10.1021/bi00597a007

Cited by 45 publications

(38 citation statements)

References 45 publications

(39 reference statements)

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“…Recently, Dr. David Kearns (private communication, and Ref. 19) informed us that a combination of absorption and fluorescence experiments on EtdBr binding to tRNAPhe in his laboratory suggested the existence of one strong binding site with a fluorescence lifetime of about 30 nsec and three weaker sites with a fluorescence lifetime on the order of 5-15 nsec. These results are totally consistent with our interpretation and analysis of the thermodynamics of the interaction of EtdBr to the putative unique binding site.…”

Section: Discussionmentioning

confidence: 99%

Thermodynamic characterization of ethidium bromide binding to a unique site on a yeast tRNA^Phe

Sturgill

1978

Biopolymers

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A self‐consistent thermodynamic characterization of the binding of ethidium to yeast phenylalanine‐specific tRNA at 25°C, pH 7.0, in 11 nM MgCl2, 375 nM NaCl, and 25 mM sodium phosphate has been obtained. Two ethidium molecules bind per tRNA under these conditions. The stronger site has a dissociation constant equal to 1.9 ± 0.5 μM and ΔHdis°′ = 12 ± 1 Kcal/mol, and the weaker sites has a dissociation constant equal to 24 ± 9 μM and ΔHdis°′ = 8.9 ± 1.5 Kcal/mol. The average calorimetric ΔHdis°′ for the to sites 10.6 ± 0.4 kcal/mol. The thermodynamics of binding to the stranger sites are most probably the thermodynamics of interaction between A·U (6) and A·U (7), the unique site identified by Jones and Kearns. The binding is enthalpically driven and classical hydrophobic interactions do not appear to be important in the binding reaction.

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Section: Discussionmentioning

confidence: 99%

Thermodynamic characterization of ethidium bromide binding to a unique site on a yeast tRNA^Phe

Sturgill

1978

Biopolymers

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“…Classical DNA intercalators such as ethidium have been known for some time to interact with RNA. 35 Simple DNA binders such as Hoechst dyes 33342 and 33258 are inactive in the FRET assay (data not shown). Though the term intercalation in DNA has specific associations, which are not appropriate for RNA, some element of base-stacking between base-pairs is common to the rbt418/550 series and to DNA intercalators.…”

Section: Interaction Of Rbt550/418 Series With Tar Rnamentioning

confidence: 97%

Structure-based Drug Design Targeting an Inactive RNA Conformation: Exploiting the Flexibility of HIV-1 TAR RNA

Murchie

Davis

Isel

et al. 2004

Journal of Molecular Biology

133

138

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“…Spectrally resolved FLIM Q. S. Hanley S85 dequenching process similar to EB (Olmsted & Kearns 1977;Jones et al 1978;Leupin et al 1985). These data (figure 2) were originally published as plots of phase and modulation lifetime spectra.…”

Section: Ab-plotsmentioning

confidence: 99%

Spectrally resolved fluorescent lifetime imaging

Hanley

2008

J. R. Soc. Interface.

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Placing an imaging spectrograph or related components capable of generating a spectrum between a microscope and the image intensifier of a conventional fluorescence lifetime imaging (FLIM) system creates a spectrally resolved FLIM (SFLIM). This arrangement provides a number of opportunities not readily available to conventional systems using bandpass filters. The examples include: simultaneous viewing of multiple fluorophores; tracking of both the donor and acceptor; and observation of a range of spectroscopic changes invisible to the conventional FLIM systems. In the frequency-domain implementation of the method, variation in the fractional contributions from different fluorophores along the wavelength dimension can behave as a surrogate for a frequency sweep or spatial variations while analysing fluorophore mixtures. This paper reviews the development of the SFLIM method, provides a theoretical and practical overview of frequency-domain SFLIM including: presentation of the data; manifestations of energy transfer; observation of multiple fluorophores; and the limits of single frequency methods.

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Ethidium bromide binding to transfer RNA: transfer RNA as a model system for studying drug-RNA interactions

Cited by 45 publications

References 45 publications

Thermodynamic characterization of ethidium bromide binding to a unique site on a yeast tRNA^Phe

Thermodynamic characterization of ethidium bromide binding to a unique site on a yeast tRNA^Phe

Structure-based Drug Design Targeting an Inactive RNA Conformation: Exploiting the Flexibility of HIV-1 TAR RNA

Spectrally resolved fluorescent lifetime imaging

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Ethidium bromide binding to transfer RNA: transfer RNA as a model system for studying drug-RNA interactions

Cited by 45 publications

References 45 publications

Thermodynamic characterization of ethidium bromide binding to a unique site on a yeast tRNAPhe

Thermodynamic characterization of ethidium bromide binding to a unique site on a yeast tRNAPhe

Structure-based Drug Design Targeting an Inactive RNA Conformation: Exploiting the Flexibility of HIV-1 TAR RNA

Spectrally resolved fluorescent lifetime imaging

Contact Info

Product

Resources

About

Thermodynamic characterization of ethidium bromide binding to a unique site on a yeast tRNA^Phe

Thermodynamic characterization of ethidium bromide binding to a unique site on a yeast tRNA^Phe