Proton magnetic resonance studies of ethidium bromide and its sodium borohydride reduced derivative

Mechanistic insights into ethidium bromide removal by palygorskite from contaminated water

Ethidium bromide (EtBr)-containing wastewater can be hazardous to biodiversity when released into the soil and water bodies without treatment. EtBr can mutate living microbial cells and pose toxicity to even higher organisms. This work investigated the removal of EtBr from aqueous solutions by a naturally occurring palygorskite (PFl-1) clay mineral via systematic batch adsorption experiments under different physicochemical conditions. EtBr existed in an undissociated form at pH ~7, and was adsorbed on PFl-1 obeying the Freundlich isotherm model. The maximum EtBr adsorption capacity was 285 mmol/kg. The best fitted kinetic model for EtBr adsorption was the pseudo-second order model. The amounts of exchangeable cations desorbed from PFl-1 during EtBr adsorption was linearly correlated to the amounts of EtBr adsorbed, with a slope of 0.97, implying that a cation exchange-based adsorption mechanism was dominating. Additionally, dimerization of EtBr molecules via bromide release assisted an increased EtBr removal by PFl-1 at high adsorbate concentrations. Detailed x-ray diffraction, Fourier transform infrared, scanning electron imaging and energy dispersive x-ray analyses confirmed that EtBr adsorption occurred dominantly on the surface of palygorskite which mineralogically constituted 80% of the bulk PFl-1 adsorbent. A small portion of EtBr was also adsorbed by PFl-1 through intercalation onto the smectite impurity (10%) in PFl-1. This study suggested that PFl-1 could be an excellent natural material for removing EtBr from pharmaceutical and laboratory wastewater.

Enhanced removal of ethidium bromide (EtBr) from aqueous solution using rectorite

Ethidium bromide (EtBr) is an intercalating agent commonly used as nucleic acid fluorescent tag in various techniques of life science field. It is considered as a serious biohazard due to its mutagenicity and carcinogenicity. As such, developing high efficiency and low cost materials as cleanup kits is in urgent need although many methods have already been developed. In this study we take use of the affinity of organic cations for clay minerals of high cation exchange capacity (CEC) and large specific surface area (SSA) and tested the removal of EtBr using rectorite, a type of clay mineral made of 1:1 regularly mixed layers of illite and montmorillonite. Our results showed that the uptake of Et⁺ on rectorite could be as high as 400 mmol/kg and the removal of Et⁺ was extremely fast. Desorption of inorganic cation Ca²⁺ and sorption of counterion Br^- revealed that cation exchange was the dominating mechanism of Et⁺ removal using rectorite. Thermal analyses revealed that the EtBr could be thermally destructed inside the interlayer of rectorite and the material could be thermally regenerated. Thus, clay minerals could have a great potential to be fabricated into cleanup kits for the removal of EtBr in case of spill.

Evaluation of a novel radiotracer for positron emission tomography imaging of reactive oxygen species in the central nervous system

INTRODUCTION

Few, if any, radiotracers are available for the in vivo imaging of reactive oxygen species (ROS) in the central nervous system. ROS play a critical role in normal cell processes such as signaling and homeostasis but overproduction of ROS is implicated in several disorders. We describe here the radiosynthesis and initial ex vivo and in vivo evaluation of [¹¹C]hydromethidine ([¹¹C]HM) as a radiotracer to image ROS using positron emission tomography (PET).

METHODS

[¹¹C]HM and its deuterated isotopologue [¹¹C](4) were produced using [¹¹C]methyl triflate in a one-pot, two-step reaction and purified by high performance liquid chromatography. Ex vivo biodistribution studies were performed after tail vein injections of both radiotracers. To demonstrate sensitivity of uptake to ROS, [¹¹C]HM was administered to rats treated systemically with lipopolysaccharide (LPS). In addition, ex vivo autoradiography and in vivo PET imaging were performed using [¹¹C]HM on rats which had been microinjected with sodium nitroprusside (SNP) to induce ROS.

RESULTS

[¹¹C]HM and [¹¹C](4) radiosyntheses were reliable and produced the radiotracers at high specific activities and radiochemical purities. Both radiotracers demonstrated good brain uptake and fast washout of radioactivity, but [¹¹C](4) washout was faster. Pretreatment with LPS resulted in a significant increase in brain retention of radioactivity. Ex vivo autoradiography and PET imaging of rats unilaterally treated with microinjections of SNP demonstrated increased retention of radioactivity in the treated side of the brain.

CONCLUSIONS

[¹¹C]HM has the attributes of a radiotracer for PET imaging of ROS in the brain including good brain penetration and increased retention of radioactivity in animal models of oxidative stress.

Chromatographic and spectroscopic analysis of the components present in the phenanthridinium trypanocidal agent isometamidium

The chromatographic isolation and characterisation of the four compounds present in the quaternary phenanthridine veterinary trypanocidal agent, isometamidium chloride hydrochloride (ISM), is reported. The isolated compounds were unambiguously characterised using spectroscopic (NMR, UV, IR and MS) methods as 3-amino-8-[3-(3-carbamimidoyl-phenyl)-triazenyl]-5-ethyl-6-phenylethidium (1a) and related isomers, 8-amino-3-[3-(3-carbamimidoyl-phenyl)-triazenyl]-5-ethyl-6-phenylethidium, 3,-8-diamino-7-[3-(3-carbamimidoyl-phenyl)-triazenyl]-5-ethyl-6-phenylethidium and 3,-8-bis[3-(3-carbamimidoyl-phenyl)-triazenyl]-5-ethyl-6-phenylethidium. During the course of this study, it was realised that the nature of the solvent used in the NMR study was critical as in DMSO-d6 the quaternary group in the compounds was reduced to dihydro forms (e.g. 2a).

AMPK dysregulation promotes diabetes-related reduction of superoxide and mitochondrial function

Diabetic microvascular complications have been considered to be mediated by a glucose-driven increase in mitochondrial superoxide anion production. Here, we report that superoxide production was reduced in the kidneys of a steptozotocin-induced mouse model of type 1 diabetes, as assessed by in vivo real-time transcutaneous fluorescence, confocal microscopy, and electron paramagnetic resonance analysis. Reduction of mitochondrial biogenesis and phosphorylation of pyruvate dehydrogenase (PDH) were observed in kidneys from diabetic mice. These observations were consistent with an overall reduction of mitochondrial glucose oxidation. Activity of AMPK, the major energy-sensing enzyme, was reduced in kidneys from both diabetic mice and humans. Mitochondrial biogenesis, PDH activity, and mitochondrial complex activity were rescued by treatment with the AMPK activator 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR). AICAR treatment induced superoxide production and was linked with glomerular matrix and albuminuria reduction in the diabetic kidney. Furthermore, diabetic heterozygous superoxide dismutase 2 (Sod2(+/-)) mice had no evidence of increased renal disease, and Ampka2(-/-) mice had increased albuminuria that was not reduced with AICAR treatment. Reduction of mitochondrial superoxide production with rotenone was sufficient to reduce AMPK phosphorylation in mouse kidneys. Taken together, these results demonstrate that diabetic kidneys have reduced superoxide and mitochondrial biogenesis and activation of AMPK enhances superoxide production and mitochondrial function while reducing disease activity.

Detection of inflammatory processes during various diseases by the method of flow cytofluorometry

Oxidative (respiratory) burst is an important manifestation of inflammation. Precise quantitative assessment of this reaction by flow cytometry made it possible to record and evaluate the severity of the inflammatory processes in a wide spectrum of diseases including diphtheria, hepatitis, pneumonia, bronchial asthma, arthritis, vasculitis, postoperative complications, tuberculosis, psoriasis, rheumatoid arthritis, systemic lupus erythematosus, and myocardial infarction. This approach can be employed as a highly sensitive method of detection of inflammatory reactions and monitoring of their course in various pathological processes.

Curcumin supplementation could improve diabetes-induced endothelial dysfunction associated with decreased vascular superoxide production and PKC inhibition

Background

Curcumin, an Asian spice and food-coloring agent, is known for its anti-oxidant properties. We propose that curcumin can improve diabetes-induced endothelial dysfunction through superoxide reduction.

Methods

Diabetes (DM) was induced in rats by streptozotocin (STZ). Daily curcumin oral feeding was started six weeks after the STZ injection. Twelve weeks after STZ injection, mesenteric arteriolar responses were recorded in real time using intravital fluorescence videomicroscopy. Superoxide and vascular protein kinase C (PKC-βII) were examined by hydroethidine and immunofluorescence, respectively.

Results

The dilatory response to acetylcholine (ACh) significantly decreased in DM arterioles as compared to control arterioles. There was no difference among groups when sodium nitroprusside (SNP) was used. ACh responses were significantly improved by both low and high doses (30 and 300 mg/kg, respectively) of curcumin supplementation. An oxygen radical-sensitive fluorescent probe, hydroethidine, was used to detect intracellular superoxide anion (O₂^●-) production. O₂^●- production was markedly increased in DM arterioles, but it was significantly reduced by supplementation of either low or high doses of curcumin. In addition, with a high dose of curcumin, diabetes-induced vascular PKC-βII expression was diminished.

Conclusion

Therefore, it is suggested that curcumin supplementation could improve diabetes-induced endothelial dysfunction significantly in relation to its potential to decrease superoxide production and PKC inhibition.

HPLC study of oxidation products of hydroethidine in chemical and biological systems: ramifications in superoxide measurements

Methods for the detection and quantitation of hydroethidine (HE) and its oxidation products by HPLC analysis are described. Synthetic methods for preparation of authentic standards (2-hydroxyethidium and diethidium) are provided. Potential applications of the HPLC methods to chemical and biological systems are discussed. Specific examples of chromatograms obtained using UV-Vis absorption, fluorescence, electrochemical, and mass spectrometry detectors are provided. The development of a dual electrochemical and fluorescence detection methodology and its applications are described. The HPLC-based method enables analyses of HE and its oxidation products such as ethidium and the dimeric products of HE. The ramifications of HPLC measurement of HE and its oxidation products in the detection and quantitation of 2-hydroxyethidium, the diagnostic marker product of superoxide and HE, in the intracellular milieu are discussed. Similarly, mitochondria-targeted HE conjugated to a triphenylphosphonium group (Mito-HE or Mito-SOX) also forms oxidation products (dimers of Mito-HE and Mito-E+) that can affect the detection and quantitation of 2-hydroxy-mito-ethidium, the diagnostic marker product of Mito-HE and superoxide in mitochondria.

Pulse radiolysis and steady-state analyses of the reaction between hydroethidine and superoxide and other oxidants

Hydroethidine (HE) is a cell-permeable probe used for the intracellular detection of superoxide. Here, we report the direct measurement of the rate constant between hydroethidine and superoxide radical anion using the pulse radiolysis technique. This reaction rate constant was calculated to be ca. 2 x 10(6) M(-1) s(-1) in water:ethanol (1:1) mixture. The spectral characteristics of the intermediates indicated that the one-electron oxidation product of HE was different from the one-electron reduction product of ethidium (E+). The HPLC-electrochemical measurements of incubation mixtures containing HE and the oxygenated Fenton's reagent (Fe2+/DTPA/H2O2) in the presence of aliphatic alcohols or formate as a superoxide generating system revealed 2-OH-E+ as a major product. Formation of 2-OH-E+ by the Fenton's reagent without additives was shown to be superoxide dismutase-sensitive and we attribute the formation of superoxide radical anion to the one-electron reduction of oxygen by the DTPA-derived radical. Addition of tert-butanol, DMSO, and potassium bromide to the Fenton's system caused inhibition of 2-OH-E+ formation. Results indicate that reducing and oxidizing radicals have differential effects on the formation of 2-OH-E+.

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.

Mechanistic similarities between oxidation of hydroethidine by Fremy's salt and superoxide: stopped-flow optical and EPR studies

We have previously shown that superoxide radical anion (O2.-) reacts with hydroethidine (HE) to form a product that is distinctly different from ethidium (E+) (Zhao et al., Free Radic. Biol. Med. 34:1359; 2003). The structure of this product was recently determined as the 2-hydroxyethidium cation (2-OH-E+) (Zhao et al., Proc. Natl. Acad. Sci. USA 102:5727; 2005). In this study, using HPLC and mass spectrometry techniques, we show that 2-OH-E+ is formed from the reaction between HE and nitrosodisulfonate radical dianion (NDS) or Fremy's salt. The reaction kinetics and mechanism were determined using steady-state and time-resolved optical and EPR techniques. Within the first 50 ms, an intermediate was detected. Another intermediate absorbing strongly at 460 nm and weakly at 670 nm was detected within a second. The structure of this species was assigned to an imino quinone derivative of HE. The stoichiometry of the reaction indicates that two molecules of NDS were needed to oxidize a molecule of HE. We postulate that the first step of the reaction involves the hydrogen atom abstraction from HE to form an aminyl radical that reacts with another molecule of NDS to form an adduct that decomposes to an imino quinone derivative of HE. A similar mechanism has been proposed for the reaction between HE and O2.-. The reaction between HE and the Fremy's salt should provide a facile route for the synthesis of 2-OH-E+, a diagnostic marker product of the HE/O2.- reaction.

Detection and characterization of the product of hydroethidine and intracellular superoxide by HPLC and limitations of fluorescence

Here we report the structural characterization of the product formed from the reaction between hydroethidine (HE) and superoxide (O(2)(.-)). By using mass spectral and NMR techniques, the chemical structure of this product was determined as 2-hydroxyethidium (2-OH-E(+)). By using an authentic standard, we developed an HPLC approach to detect and quantitate the reaction product of HE and O(2)(.-) formed in bovine aortic endothelial cells after treatment with menadione or antimycin A to induce intracellular reactive oxygen species. Concomitantly, we used a spin trap, 5-tert-butoxycarbonyl-5-methyl-1-pyrroline N-oxide (BMPO), to detect and identify the structure of reactive oxygen species formed. BMPO trapped the O(2)(.-) that formed extracellularly and was detected as the BMPO-OH adduct during use of the EPR technique. BMPO, being cell-permeable, inhibited the intracellular formation of 2-OH-E(+). However, the intracellular BMPO spin adduct was not detected. The definitive characterization of the reaction product of O(2)(.-) with HE described here forms the basis of an unambiguous assay for intracellular detection and quantitation of O(2)(.-). Analysis of the fluorescence characteristics of ethidium (E(+)) and 2-OH-E(+) strongly suggests that the currently available fluorescence methodology is not suitable for quantitating intracellular O(2)(.-). We conclude that the HPLC/fluorescence assay using HE as a probe is more suitable [corrected] for detecting intracellular O(2)(.-).

Superoxide reacts with hydroethidine but forms a fluorescent product that is distinctly different from ethidium: potential implications in intracellular fluorescence detection of superoxide

Hydroethidine (HE) or dihydroethidium (DHE), a redox-sensitive probe, has been widely used to detect intracellular superoxide anion. It is a common assumption that the reaction between superoxide and HE results in the formation of a two-electron oxidized product, ethidium (E+), which binds to DNA and leads to the enhancement of fluorescence (excitation, 500-530 nm; emission, 590-620 nm). However, the mechanism of oxidation of HE by the superoxide anion still remains unclear. In the present study, we show that superoxide generated in several enzymatic or chemical systems (e.g., xanthine/xanthine oxidase, endothelial nitric oxide synthase, or potassium superoxide) oxidizes HE to a fluorescent product (excitation, 480 nm; emission, 567 nm) that is totally different from E+. HPLC measurements revealed that the HE/superoxide reaction product elutes differently from E+. This new product exhibited an increase in fluorescence in the presence of DNA. Mass spectral data indicated that the molecular weight of the HE/superoxide reaction product is 330, while ethidium has a molecular weight of 314. We conclude that the reaction between superoxide and HE forms a fluorescent marker product that is different from ethidium. Potential implications of this finding in intracellular detection and imaging of superoxide are discussed.

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.

Synthesis and biologic studies of iodinated (125I/127I) ethidium

An iodinated (125I/127I) ethidium derivative (3,8-diamino-5-[6'-(p-iodobenzoylamino)-4'-azahexyl]-6-phenylphenanthridinium chloride hydrochloride) was synthesized and characterized. The labeling yield of the 125I-labeled derivative was 75% for carrier-free 125I, with a radiochemical purity of 95%. The incubation of iodoethidium with calf thymus DNA resulted in a substantial enhancement of fluorescence yield, indicating the intercalation of this compound into DNA. In the presence of iodoethidium, the nuclei of methanol-treated mammalian cells fluoresced, while those of viable cells did not (since the plasma membrane is impermeable to iodoethidium). When viable cells were incubated with the reduced form of the derivative, 125I/127I-dihydroethidium traversed the plasma membrane, was oxidized in the cytoplasm, and intercalated into nuclear DNA. Finally, we tested the hypothesis that larger malignant solid tumors, containing a relatively greater percentage of degenerating permeable cells, can be targeted with 125I-ethidium. In-vivo studies demonstrated a small but positive correlation (R = 0.72) between tumor volume and the uptake of the derivative. Because of the ubiquitous presence of abnormal permeable cells and necrosis in tumors, our results support the belief that radiolabeled DNA-intercalating or DNA-binding molecules may be of diagnostic and therapeutic value for a variety of solid tumors in humans.

Energetics of DNA intercalation reactions

Isothermal titration calorimetry has been used to determine the binding enthalpy and heat capacity change (DeltaC(p)()) for a series of DNA intercalators, including ethidium, propidium, daunorubicin, and adriamycin. Temperature-dependent binding enthalpies were measured directly for the ligands, from which DeltaC(p)() values of -140 to -160 cal mol(-)(1) K(-)(1) were calculated. Published van't Hoff plots were reanalyzed to obtain DeltaC(p)() values of -337 to -423 cal mol(-)(1) K(-)(1) for the binding of actinomycin D to several DNA oligonucleotide duplexes with defined sequences. Heat capacity changes for DNA intercalation were found to correlate with the alterations in solvent-accessible surface area calculated from available high-resolution structural data. Multiple linear regression was used to derive the relationship DeltaC(p)() = 0. 382(+/-0.026)DeltaA(np) - 0.121(+/-0.077)DeltaA(p) cal mol(-)(1) K(-)(1), where DeltaA(np) and DeltaA(p) are the binding-induced changes in nonpolar and polar solvent-accessible surface areas (in square angstroms), respectively. The DeltaC(p)() terms were used to estimate the hydrophobic contribution to intercalative binding free energies, yielding values that ranged from -11.2 (ethidium) to -30 kcal mol(-)(1) (actinomycin D). An attempt was made to parse the observed binding free energies of ethidium and propidium into five underlying contributions. Such analysis showed that the DNA binding behavior of these simple intercalators is driven almost equally by hydrophobic effects and van der Waals contacts within the intercalation site.

In vivo evidence for microvascular oxidative stress in spontaneously hypertensive rats. Hydroethidine microfluorography

The factors that predispose to the accelerated organ injury that accompanies the hypertensive syndrome have remained speculative and without a firm experimental basis. Indirect evidence has suggested that a key feature may be related to an enhanced oxygen radical production. The purpose of this study was to refine and use a technique to visualize evidence of spontaneous microvascular oxidative stress in vivo in the spontaneously hypertensive rat (SHR) compared with its normotensive control, the Wistar-Kyoto rat (WKY). We investigated the effects of adrenal glucocorticoids on the microvascular oxidative stress sequence. The mesentery was superfused with hydroethidine, a reduced, nonfluorescent precursor of ethidium bromide. In the presence of oxidative challenge, hydroethidine is transformed intracellularly into the fluorescent compound ethidium bromide, which binds to DNA and can be detected by virtue of its red fluorescence. The fluorescent light emission from freshly exteriorized and otherwise unstimulated mesentery microvessels was recorded by digital microscopy. The number of ethidium bromide-positive nuclei along the arteriolar and venular walls in SHR was found to be significantly increased above the level exhibited by WKY. The elevation in ethidium bromide fluorescence in SHR arterioles could be attenuated by a synthetic glucocorticoid inhibitor and in rats subjected to adrenalectomy. The administration of glucocorticoids after adrenalectomy by injection of dexamethasone restored the oxidative reaction in SHR arterioles. Treatment with dimethylthiourea and with a xanthine oxidase inhibitor attenuated the superoxide formation. Although a nitric oxide synthase inhibitor (NG-nitro-L-arginine methyl ester) enhanced the ethidium bromide staining in WKY, it did not affect that in SHR.(ABSTRACT TRUNCATED AT 250 WORDS)

The interaction between prothidium dibromide and DNA at the molecular level

The interactions in solution and in the fibre state of the trypanocidal drug, prothidium dibromide, with DNA have been investigated using a number of biophysical techniques. The binding parameters at 0.11 ionic strength were determined by spectroscopic means. Sedimentation studies show that the drug is able to unwind closed circular DNA in solution, but X-ray diffraction and linear dichroism experiments indicate that it is uncertain whether this unwinding can be attributed to intercalation in the classical sense. On the basis of our results, we propose that the primary mode of binding is "sideways" intercalation, supplemented by electrostatic binding along the sugar-phosphate chains and interstrand binding involving hydrogen bonding.

A comparison of the base-pair specificities of three phenanthridine drugs using solution spectroscopy

1. The absorption spectrum of three phenanthridine drugs (ethidium, dimidium and prothidium bromide) bound to natural DNAs of differing G-C content were obtained using a novel mixing scheme and analysed according to the excluded site binding model. 2. Ethidium bromide shows a strong G-C specificity at low binding ratios. especially at low ionic concentration. 3. Dimidium bromide shows a less strong G-C specificity. 4. For both drugs, the binding site size reflects a situation close to nearest-neighbour exclusion. 5. Prothidium shows no specificity in its binding. The binding modes are different than for the other two phenanthridines, and it is suggested that the primary mode is "sideways" intercalation.

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.

PMR studies of the self-association of DNA intercalating ellipticine derivatives in aqueous solution

In aqueous solution DNA intercalating ellipticine derivatives aggregate in n-mers. The self-association constants K are higher than those of 2-methoxy-6-chloro-9-[3-dimethylaminopropyl-amino]-acridine and ethidium bromide. They are of the same order as that of actinomycin D but inferior to that of acridine orange. The increase of the 9-hydroxy-ellipticine constant by addition of sodium chloride shows the importance of anion participation in the mechanism of stacking in accordance with the high energy of self-association. In the stacked n-mers the ellipticine rings are inverted. The geometry shows the importance of the orientation of the quadrupole axis in the intermolecular association of the intercalating drugs.

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.