Proton magnetic resonance study of the interaction of ethidium bromide with several uracil residues, uridylyl (3' leads to 5') uridine and polyuridylic acid

MitoNeoD: A Mitochondria-Targeted Superoxide Probe

Mitochondrial superoxide (O₂^⋅-) underlies much oxidative damage and redox signaling. Fluorescent probes can detect O₂^⋅-, but are of limited applicability in vivo, while in cells their usefulness is constrained by side reactions and DNA intercalation. To overcome these limitations, we developed a dual-purpose mitochondrial O₂^⋅- probe, MitoNeoD, which can assess O₂^⋅- changes in vivo by mass spectrometry and in vitro by fluorescence. MitoNeoD comprises a O₂^⋅--sensitive reduced phenanthridinium moiety modified to prevent DNA intercalation, as well as a carbon-deuterium bond to enhance its selectivity for O₂^⋅- over non-specific oxidation, and a triphenylphosphonium lipophilic cation moiety leading to the rapid accumulation within mitochondria. We demonstrated that MitoNeoD was a versatile and robust probe to assess changes in mitochondrial O₂^⋅- from isolated mitochondria to animal models, thus offering a way to examine the many roles of mitochondrial O₂^⋅- production in health and disease.

On the electronic structure of ethidium

The electronic structure of the common intercalating agent ethidium bromide (3,8-diamino-5-ethyl-6-phenylphenanthridinium bromide) is dominated by an interplay of electron donating and withdrawing effects mediated by its nitrogen atoms. X-ray crystallography, UV/Vis and IR absorption, fluorescence emission, and NMR spectroscopy are used to probe the electronic properties of the phenanthridinium "core" of ethidium as well as its exocyclic amines and 6-phenyl groups. Interestingly, despite its positive charge, most of ethidium's aromatic carbon and hydrogen atoms have high electron densities (compared to both 6-phenylphenanthridine and benzene). The data suggest that electron donation by ethidium's exocyclic amines dominates over the electron withdrawing effects of its endocyclic iminium in their combined influence on the electron densities of these atoms. Ethidium's nitrogen atoms are, conversely, electron deficient where the 5-position is the most electropositive, followed by the 3-amino, and lastly the 8-amino group. These results have been used to generate an empirically-based pi-electron density map of ethidium that may prove useful to understanding its nucleic acid binding specificity.

Spectroelectrochemistry study on the electrochemical reduction of ethidium bromide

The electrochemical reduction mechanism of ethidium bromide was first studied by spectroelectrochemistry. This reduction was proved to be a two-step process by cyclic voltammetry, differential pulse voltammetry and spectroelectrochemistry, in which each step was proved to be a one-electron transfer process by a spectropotentiostatic fluorescence technique. Hydroethidine was confirmed to be the final product by comparing the spectrum of the product of the electrochemical reduction to that of the product of the chemical reduction of ethidium bromide, and a carbon-centered radical was concluded to be a reasonable intermediate product during the electrochemical reduction of ethidium bromide.

Localization of the major ethidium bromide binding site on tRNA

Binding of ethidium bromide to Escherichia coli tRNAVal and an RNA minihelix based on the acceptor stem and T-arm of tRNAVal was investigated by 19F and 1H NMR spectroscopy of RNAs labeled with fluorine by incorporation of 5-fluorouracil. Ethidium bromide selectively intercalates into the acceptor stem of the tRNAVal. More than one ethidium bromide binding site is found in the acceptor stem, the strongest between base pairs A6:U67 and U7:A66. 19F and 1H spectra of the 5-fluorouracil-substituted minihelix RNA indicate that the molecule exists in solution as a 12 base-paired stem and a single-stranded loop. Ethidium bromide no longer intercalates between base pairs corresponding to the tRNAVal acceptor stem in this molecule. Instead, it intercalates between base pairs at the bottom of the long stem-loop structure. These observations suggest that ethidium bromide has a preferred intercalation site close to the base of an RNA helical stem.

Ethidium bromide binding to unstructured and structured 2' GMP

For disordered 2' GMP and 5' GMP the ethidium cation (Etd) was found to form 1:1 and 2:1 Eth:nucleotide complex. For alkali metal solution self-structured 2'GMP and 5'GMP Etd was found to form 1:1 and 2:1 Etd: order nucleotide complex. The best computer fit was obtained for a structured nucleotide stoichiometry of Na4(2'GMP)8. Binding constants for the Etd:disordered 2'GMP complexes were determined to be (1.6 +/- 0.1) x 10(4)M(-1) and 6.3 +/- 0.5 M(-1) at O degrees C and (1.1 +/- 0.2) x 10(4) M(-1) and 18 +/- 11M(-1) for 5'GMP at 5 degrees C for the 1:1 and 1:2 complex, respectively. For the 1:1 and 1:2 2'GMP:Etd species the enthalpies were determined to be -19.8 +/- 1.0 kcal/mole and 0.1 +/- 0.3 kcal/mole, respectively, and the entropies were -53.3 +/- 6.6 eu and 3.9 +/- 1.6 eu, respectively. Binding constants for the Etd: structured 2'GMP complex, assuming a complex with stoichoimetry (Na+)4 (2'GMP)8 for the structured unit, were determined to be (1.9 +/- 0.1) x 10(4)M(-1) and 5.8 +/- 0.6) x 10(2)M(-1), respectively at 0 degrees C.

Interactions of a fragment of bleomycin with deoxyribodinucleotides: nuclear magnetic resonance studies

Proton NMR spectroscopy was used to establish certain geometrical parameters of the complexes formed between N-(3-aminopropyl)-2'-(2-acetamidoethyl)-2,4'-bithiazole-4-carboxamide hydrochloride (BLMF), a fragment of bleomycin, and various deoxyribodinucleotides. All proton resonances in these compounds have been assigned; chemical shifts were recorded as functions of their concentration. In the complex formed between BLMF and pdG-dC, chemical shifts of the bithiazole protons (measured with respect to values extrapolated to infinite dilution) were displaced upfield by 0.4 ppm. Other proton resonances of BLMF were shifted upfield but to a lesser extent. After corrections are made for self-stacking, maximum values for induced chemical shifts of the bithiazole protons are reached at a dinucleotide/BLMF ratio of 2. Coupling sums for dinucleotides (12.5-13.7 Hz) were unchanged following complexation, suggesting that there is no marked change in sugar conformation when BLMF is bound. On the basis of these results and of molecular model building studies, we propose a three-dimensional structure for a BLMF:pdG-dc complex in which the thiazole rings are intercalated in the duplex and stack preferentially on the purines. Projected on the same plane, the horizontal axis connecting the center of both bithiazole rings in this configuration superimposes on the axis connecting the centers of the purine bases. In this complex, both thiazole protons extend into the minor groove and the positively charged terminal amine binds to the negatively charged phosphate group of DNA.

Comparative viscometric analysis of the interaction of chloroquine and quinacrine with superhelical and sonicated DNA

Unwinding angles for the structurally related antimalarial drugs chloroquine and quinacrine have been determined with superhelical Col E1 plasmid DNA by applying the quantitative method developed by Vinograd and co-workers (Revet, B.M., Schmir, M. and Vinograd, J. (1971) Nat. New Biol. 229, 10). The value for chloroquine, 8.6 degrees, calculated assuming an unwinding angle of 26 degrees for ethidium bromide, is significantly lower than the value for quinacrine, 22.5 degrees, calculated in the same manner. Viscometric titrations with sonicated calf thymus DNA were quantitated using available binding constants for the two drugs and indicated that chloroquine also causes significantly smaller DNA length increases on intercalation relative to quinacrine. The conclusion from these experiments is that chloroquine does not bind to DNA by the classical intercalation mechanism typical of quinacrine and ethidium.

Direct physical measurements on substituted agarose gels: evidence for intercalation of gel-bound ethidium into transfer RNA

The cation of the salt ethidium bromide (3,8-diamino-5-ethyl-6-phenylphenanthridinium bromide) has been covalently linked to an agarose matrix through an intermediate 3,3'-diaminodipropylaminosuccinyl spacer arm. Partition binding and visible absorption spectral measurements on the gel were used to monitor the binding of transfer RNA to the covalently bound ethidium group. Direct fluorescence measurements of the formation of the gel-bound complex indicate that this binding involves the intercalation of the ethidium groups into the tRNA molecule. Dissociation of the ethidium-tRNA complex was monitored as a function of sodium chloride concentration by both direct solution spectral measurement of the released tRNA and by fluorescence quenching measurements of the dissociation of the intercalation complex. The derivatized gel has been shown to be capable of the fractionation of tRNA species by elution with a positive salt gradient under column flow conditions.

The interaction of propidium diiodide with self-complementary dinucleoside monophosphates

The interactions of a quinacrine derivative, methylated at both the aromatic and aliphatic nitrogens, and propidium diiodide with the dinucleoside monophosphates CpG, GpC, UpA and ApU have been investigated using 13C-NMR (for the quinacrine derivative prepared with [13C]methyl substituents and 1H-NMR and ultraviolet-visible spectroscopy. The quinacrine derivative displayed negligible interaction with the dinucleosides at concentrations up to 5 - 10(-4) M. Propidium did form complexes with dinucleosides even at concentrations as low as 10(-4) M. Propidium displayed a pyrimidine-purine binding preference and gave especially large changes in ultraviolet-visible and 1H-NMR spectra in the presence of CpG. This suggests that propidium forms an intercalated complex with a Watson-Crick hydrogen-bonded CpG dimer. At higher concentrations UpA and GpC gave similar spectral changes indicating that they could also form significant amounts of an intercalated complex with propidium under appropriate conditions. The changes caused by ApU were small under all conditions and were more similar to the effects caused by mononucleotides. These results indicate that, at least for phenanthridines, cationic side chains do not greatly inhibit complex formation with dinucleoside monophosphates, and suggest that the weak interaction of the quinacrine derivative with dinucleosides is due to weaker interactions of the acridine ring system with nucleoside bases relative to the phenanthridine ring system.

Synthesis, separation and characterization of the mono- and diazide analogs of ethidium bromide

Ethidium bromide is used to characterize nucleic acid secondary and tertiary structural properties and the biological consequences of drug interactions. The mono- and diazido analogs of ethidium have proven valuable as photoaffinity probes in chemical and biological studies on nucleic acids, since they render the ethidium-nucleic acid interaction covalent. Although both of these compounds have been synthesized previously, the published synthesis procedure for the monoazide is inadeqlate since a major portion of the product has been identified as the diazide analog. This lack of purity severely limits the usefulness for nucleic acid research. The procedure presented here for the synthesis, separation, purification and crystallization of these analogs should provide the quantities and quality of these important reagents needed to perform a variety of chemical and biological experiments.

Kinetic studies of drug-dinucleotide complexes

Three classes of kinetic behavior are observed in the complexes of actinomycin or ethidium with deoxydinucleotides. First, the initial dinucleotide binding to form a 1:1 complex is a rapid bimolecular process, whose rate could be measured for combination of actinomycin with d(pTpG) d(pGpT), d(pGpA), d(pGpG) d(pCpGpG), and d(pCpG) andfor combination of ethidium with d(pGpC). Second, with one exception, all reactions in which a second dinucleotide is added to form a 2:1 dinucleotide-drug complex are limited by a first-order step at high concentration. This class includes the combination of actinomycin with all dinucleotides tested except d(pGpC), and the reaction of ethidium with nucleotides of complementary sequence pyrimidine-purine, such as d(pCpG). The final class is the special case of d(pGpC) interacting to form a 2:1 complex with actinomycin. Third-order kinetics is observed, with no evidence for a first-order, rate-limiting step.

Ethidium bromide-(dC-dG-dC-dG)2 complex in solution: intercalation and sequence specificity of drug binding at the tetranucleotide duplex level

The binding of ethidium bromide (EtdBr) to the dC-dG-dC-dG self-complementary duplex has been monitored at the resolvable drug and nucleic acid protons and backbone phosphates at high nucleotide/drug (N/D) ratios by nuclear magnetic resonance (NMR) spectroscopy in aqueous solution. We observe averaged resonances (25 degrees-95 degrees) for the nucleic acid and drug nonexchangeable protons in the presence of excess tetranucleotide (N/D = 24), indicative of rapid exchange relative to the chemical shifts in the free and complexed states. Complex formation results in upfield shifts for the base protons at the terminal and internal base pairs and an increase in the transition midpoint for the duplex-to-strand conversion. We observe upfield chemical shift changes of 1.2 ppm at the Watson-Crick guanine N-1 proton(s) on complex formation (N/D = 24), with slow exchange between (dC-dG-dC-dG)2 and EtdBr-(dC-dG-dC-dG)2 relative to this chemical shift difference at-5 degrees. The EtdBr phenanthridine ring protons shift upfield by about 0.9 ppm (H-2, H-4, H-7, H-9) and greater than 0.5 ppm (H-1, H-10) on complex formation, with the chemical shifts versus temperature plots (25 degrees-95 degrees) monitoring the dissociation of the EtdBr-(dC-dG-dC-dG)2 structure. These upfield shifts at the exchangeable and nonexchangeable base protons and phenanthridine ring (but not side chain) protons demonstrate intercalation of the phenanthridine ring of EtdBr into the dC-dG-dC-dG duplex in solution. The intercalation model may be supported by the observation of downfield shifts (up to 1ppm) at the internucleotide phosphate(s) of the tetranucleotide duplex on addition of EtdBr at low temperatures. We observe stronger binding of EtdBr to the self-complementary dC-dG-dC-dG (2 dC-dG intercalation sites) and dC-dC-dG-dG (1 dC-dG site) duplexes compared to the dG-dG-dC-dC (no dC-dG sites) as monitored by UV absorbance changes at 480 nm. These studies extend to the tetranucleotide duplex level earlier observations that EtdBr exhibits a selectivity for formation of complexes to dinucleoside monophosphates with a pyrimidine (3'-5') purine sequence in the crystal and in solution. The experimental proton NMR upfield shifts at the phenanthridine protons on formation of the EtdBr-(dC-dG-dC-dG)2 complex compare favorably with calculated values (atomic diamagnetic anisotropy and ring current contributions) based on the overlap geometry for EtdBr intercalated into the pyrimidine (3'-5') purine dinucleoside monophosphate duplex in the crystal.

The secondary structure and poly(A) content of globin messenger RNA as a pure RNA and in polyribosome-derived ribonucleoprotein complexes

The conformation in solution of duck and rabbit globin mRNA, and of the duck mRNA in the mRNA - protein particle, has been investigated by optical methods and also by the use of the dye ethidium bromide which becomes highly fluorescent when intercalated into the double-stranded regions of a nucleic acid. On the basis of the properties of this dye and on the ability of homopolyribonucleotides to form double-stranded structures we have, in addition, developed a simple and sensitive assay for the detection and quantitisation of sequences rich in a particular residue that may be present in an RNA chain. In solution, 45 to 60% of the nucleotides of duck globin nRNA were found to be in bihelical regions. A similar degree of secondary structure was found in rabbit globin mRNA (this paper), as well as in calf lens mRNA and mRNAs from ewe mammary gland (other results). All samples of globin mRNA examined in this work containeda sequence of poly(A), which has poly(U) binding properties similar to that of synthetic poly(a): no specific interaction between the poly(A) sequence and the rest of the molecules can be detected. The fraction of adenosine residues within these poly(A) segments represents 4% in rabbit mRNA and 8 to 9% in duck mRNA. An additional adenosine-rich segment interspersed with guanosine and possibly other residues, was also detected in one duck mRNA sample. The RNA in the duck mRNA - protein particle is also highly structured. The melting profile in the range of 20 to 65 degrees C is quite similar to that of free mRNA and the ability of ethidium bromide to intercalate is reduced to the extent of 70%. Yet the dichroic spectra of free and bound mRNA are significantly distinct. These data suggest that free and protein-bound mRNA May have a very similar degree of secondary structure but with distinct detailed conformation in bihelical regions (change in base tilting for example). Direct evidence has been obtained that proteins stick to the poly(A) segment in the particle since the fraction of adenosine residues detectable by our poly(u) titration procedure is reduced to 50% of that observed in the free mRNA.