Ethidium bromide, binding

Esters, see Carboxylate esters Phosphate diesters Phosphate esters Ethidium bromide, binding with DNA, 186-187, 188/, 189-190... 

Fluorescent stains such as DAPI and ethidium bromide bind to DNA (sometimes even mitochondrial DNA) and have many uses, including location of nuclei and rapid detection of microorganisms or virus formation (22). The lipophilic stain DiOC(6) can be used to stain mitochondria and endoplasmic reticulum in living cells (23,24), and is also a potential-sensitive stain. 

Two types of single-stranded, intramolecular triple helices of the type shown in Figure 12(d) are possible by double-hairpin formation [37]. This was demonstrated for the R RY motif by the design of suitable 18-mer sequences containing two G tracts to fold in an antiparallel fashion. The salient features of this intramolecular triplex motif are that (1) Mg2+ is not essential, (2) compared to the intermolecular version, a shorter triplex stem can be formed in a much lower DNA concentration, and (3) acidic conditions are not required as it is the R-RY motif. The evidence for triplex existence came from the observation that duplex-hairpin intercalator binders such as actinomycin D, chromomycin Aj and ethidium bromide bind poorly. 

Nordmeier E. Absorption spectroscopy and dynamic and static light-scattering studies of ethidium bromide binding to calf thymus DNA implications for outside-binding and intercalation. J Phys Chem 1992 96 6045-55... 

Erard M, de Murcia G, Mazen A, Pouyet J, Champagne M, Daune M (1979) Ethidium bromide binding to core particles comparison with native chromatin. Nucleic Add Res 6 3232-3253... 

The IOti conjugated planar electronic structure, exhibiting strong fluorescence properties, can be useful for DNA interaction studies. Such is the case of some indolizinylpyridmiiim derivatives, found to interact similarly to ethidium bromide, binding in the minor groove, but having its fluorescence partially quenched [64]. 

Yonekura, N. Mutoh, M. Miyagi, Y Takushi, E. Ethidium bromide binding sites in DNA gel. Chem. Lett. 2000,954-955. 

Jones, C. R. Bolton, R H. Kearns, D. R. Ethidium bromide binding to transfer RNA transfer RNA as a model system for studying drug-RNA interactions. Biochemistry 1978,17, 601-607. 

Haag, D. Tschahargane, C. Goerttler, K. Does ethidium bromide bind selectively and stoichiometrically to nucleic acids in histological tissues. Histochemie 1971,27,119-124. 

The mechanism of interaction with DNA is suggested. Ethidium bromide (EB) displacement assay was performed. We determine the binding constant of Tb-E to DNA to be in the order of Ig K = 6.47 0.4. The bathochromic and hypsochromic effects in the absorption spectra of investigated complex were observed and the interaction is assumed to be mainly of the mono-intercalating type. 

It should be pointed out that when using ethidium bromide the sensitivity of the assays varies depending on the physical state of the nucleic acids (see Table I). Ethidium does not discriminate between RNA and DNA, although dyes are available which bind DNA exclusively, so the relative amounts of each may be determined by taking two sets of measurements. Alternatively, nucleases (DNA-ase or RNA-ase) can be used to exclusively remove one or the other in a mixture. Nucleic acids from different sources (see Table II) also show a variation in sensitivity, and the fluorescence assay lacks the selectivity of the hybridization technique. Nevertheless, for rapid screening or quality-control applications the fluorescence assay is still the method of choice. 

Ethidium bromide (1) is a widely used guest molecule (Scheme 1). The property that makes 1 a good probe for DNA binding is that its fluorescence quantum yield is very low in water and increases significantly when 1 intercalates between the base pairs of DNA.139... 

Table 1 Association (k+) and dissociation rate constants (k ) for the binding of ethidium bromide to DNA assuming a 1 1 complexation stoichiometry...

The values of the binding constants determined with different salt concentrations by equilibrium dialyses [43, 48], luminescence titrations and electrochemiluminescence [82], are all 2 or 3 orders of magnitude lower than for ethidium bromide. Therefore, a priori, they do not indicate contribution of classical intercalation into DNA as described for organic molecules and for the DPPZ, HAT and PPZ complexes. 

The scatchard technique consists of studying the difficulties encountered by a fluorescent dye, ethidium bromide (Fig. 19), with respect to its intercalation between the base pairs of DNA when the secondary structure of the macromolecule is modified by binding (or intercalation) of a drug. 

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