Comparative microcalorimetric and dilatometric analysis of the interactions of quinacrine,chloroquine, and ethidium bromide with DNA

The enthalpies of binding of chloroquine and quinacrine to DNA at different molar ratios of drug to DNA and at different ionic strengths have been measured. The limiting values obtained with quinacrine fall in the range found for typical intercalating agents (e.g., ethidium, proflavin, adriamycin), whereas the value obtained with chloroquine is always zero, independent of the ratio of drug to DNA and ionic strength. The dilatometric measurements performed on the same systems and on the ethidium–DNA system show that when ethidium and quinacrine bind to DNA at low drug/DNA ratios, a volume decrease of about 16 mL/mol of bound drug occurs. No change in volume is observed when the two drugs bind to DNA through external, electrostatic forces. The volume change can be attributed to the loss of structured water around hydrophobic moieties of the drug molecules, following intercalation. In contrast, chloroquine binding to DNA at low drug/DNA ratios is characterized by a volume change distinctly smaller than that shown by quinacrine. The low ΔV_B and ΔH_B values shown by chloroquine are discussed in terms of the mechanism of interaction with DNA.     

Comparative binding study of the interaction of quinacrine and ethidium bromide with DNA and nucleohistone

The degree of binding of quinacrine dihydrochloride and ethidium bromide to DNA and nucleohistone has been determined by direct and indirect methods.The results obtained by the equilibrium dialysis experiments have been analyzed in terms of various theoretical models and have led us to propose for the interaction of the dyes with DNA at low ionic strength a structural scheme where the external binding sites are next to the intercalative ones.The equilibrium dialysis results were used to check those obtained by the indirect methods, i.e. absorption and fluorescence titrations, and to identify the origin of the discrepancies.The comparative study of the binding of these dyes to DNA and nucleohistone has shown that the accessible part of DNA in the nucleoprotein is to some extent different from free DNA itself.     

Development of viscometric methods for studying the interaction of porphyrins with DNA

Abstract

The present paper is an overview of studying of DNA-porphyrin interactions using viscometry in combination with the spectroscopic methods. It was shown, that when porphyrins interact with DNA as an outside binder, the interaction mode and intensity does not depend on metal center, peripheral substituent’s and their positions on pyridylic ring. In case of planar porphyrins, the binding type is mainly determined by type of peripheral substituent’s and their position on the pyridylic ring. Currently, viscometry is widely used to study the interaction of porphyrins with DNA as an adjunct to other methods. Due to high accuracy and maximum sensitivity to changes in the size and shape of macromolecules, it is recommended to use viscometry as the cogent method for studying the interaction of small molecules with DNA, especially if intercalation is expected using other methods if necessary to confirm the results obtained. Abbreviations DNA deoxyribonucleic acid

H₂TAllPyP4 meso-tetra-(4N-allylpyridyl) porphyrin

H₂TAllPyP3 meso-tetra-(3N-allylpyridyl) porphyrin

H₂THOEtPyP4 meso-tetra-(4N-hydroxyethylpyridyl) porphyrin

H₂THOEtPyP3 meso-tetra-(3N-hydroxyethylpyridyl) porphyrin

UV/VIS spectrophotometry ultraviolet-visible spectrophotometry

CD spectroscopy circular dichroism spectroscopy

Communicated by Ramaswamy H. Sarma     

Analysis of cooperativity and ion effects in the interaction of quinacrine with DNA

The interaction of quinacrine with calf thymus DNA was monitored at several different ionic strengths using spectrophotometric and equilibrium dialysis techniques. The binding results can be explained, assuming each base pair is a potential binding site, using a model containing two negative cooperative effects: (1) ligand exclusion at binding sites adjacent to a filled binding site and (2) ligand–ligand negative cooperativity at adjacent filled binding sites. The logarithm of the observed equilibrium constant (K_obs) determined by this model varies linearily with log[Na⁺], as predicted by the ion condensation theory for polyelectrolytes. When the log K_obs plot is correlated for sodium release by DNA in the intercalation conformational change, the predicted number of ion pairs between the ligand and DNA is approximately two, as expected for the quinacrine dication. Even though K_obs depends strongly on ionic strength, the ligand negative cooperativity parameter ω was found to be indpendent of ionic strength within experimental error. This finding is also in agreement with the ion condensation theory, which predicts a relatively constant amount of condensed counterion on the DNA double helix over this ionic strength range. Drugs would, therefore, experience a relatively constant ionic environment when complexed to DNA even though the ionic conditions of the solvent could change considerably.     

A sedimentation study of the interaction of superhelical SV40 DNA with H1 histone.

By moving boundary sedimentation it is shown that the interaction of H1 histone with superhelical circular SV40 DNA results in the formation of giant heterogeneous aggregates. The size of these aggregates grows with increasing H1 concentration. s20,w values of some 10 000 S were measured. As compared with open relaxed circular DNA a preferential interaction of superhelical DNA with H1 histone is observed, irrespective of the sign of the superhelical turns which was reversed by the addition to DNA of ethidium bromide. The addition to the H1 complexed aggregates of ethidium bromide effects a progressive breakdown of the aggregates. Furthermore, the superhelicity of DNA is not changed by the addition of small amounts of H1 histone.     

The in vitro pharmacology of chloroquine and quinacrine

The effects of guanethidine, chloroquine and quinacrine on noradrenergic nerves have been compared in vitro using the isolated expansor secundariorum muscle of chicks. The effect of chloroquine on alpha-methyl-noradrenaline uptake by noradrenergic nerve terminals in various tissues were studied. The inhibitory action of guanethidine and quinacrine on noradrenergic nerves appeared to be mediated intraneuronally. The inhibitory action of chloroquine was readily reversible and unaffected by dexamphetamine. Chloroquine caused supersensitivity of the expansor muscle to noradrenaline by blocking its neuronal reuptake since the supersensitivity caused by denervation was not further increased by chloroquine. This was confirmed by the finding that chloroquine inhibited alpha-methylnoradrenaline uptake (Uptake1). Quinacrine did not cause supersensitivity to noradrenaline, possibly due to its direct depressant action on the expansor secundariorum muscle.     

Effect of copper ions on the photochemical activity of quinacrine and its interaction with DNA

The influence of cuprum ions on the interaction between the antimalarial drug quinacrine (QA) and DNA is studied by polarized laser luminescence spectroscopy and fluorescence microscopy at molecular and cellular levels. An alteration of quinacrine luminescence intensity in complex with DNA caused by cuprum ions is explained in terms of redistribution of QA molecules from quenching GC- to fluorescent AT-DNA binding sites due to the competition of Cu2+ with the dye. Mechanisms of component interactions in the triplex "DNA-QA-Cu2+" in model and cellular systems are shown to be in qualitative agreement. QA photodynamic activity change caused by Cu2+ action is explained on the basis of the ideas being developed.     

Testing of chloroquine and quinacrine for mutagenicity in Drosophila melanogaster

To extend the data on the mutagenic effects of intercalating agents in Drosophila melanogaster, chloroquine and quinacrine were tested for the induction of genetic damage in D. melanogaster males. Sex-linked recessive lethals and sex-chromosome loss induction were studied following treatment of adult males using a feeding technique. Our results show that both intercalating compounds increase significantly the frequency of sex-linked recessive lethals, but are unable to induce sex-chromosome loss in male germ cells under the conditions of testing.     

Kinetic studies of the interaction of synthetic RNAs with quinacrine and its analogs.

Temperature-jump relaxation method has been used to study the interaction of synthetic RNAs with quinacrine (QAC) and its analog. Two relaxation times were observed. The dependence of relaxation times on the RNA concentration and optical properties of the RNA-dye complexes suggests that (1) QAC binds to poly-(rA).poly(rU) through two bimolecular reactions including isomerization from one complex form to another and (2) the 2-methoxy group of the acridine ring plays a significant role in the isomerization.     

Spectroscopic studies of the interaction of synthetic RNAs with quinacrine and its analogs.

The interaction of synthetic RNAs with quinacrine (QAC) and its analogs has been studied by absorption, fluorescence and circular dichroism (CD) measurements. The results indicate that the 2-methoxy group of the acridine ring plays an important role in the appearance of the new absorption band upon binding of QAC to poly-(rA).poly(rU).     

Energetics of the strand separation transition in superhelical DNA.

In this paper the values of three free energy parameters governing the superhelical strand separation transition are determined by analysis of available experimental data. These are the free energy, a, needed to initiate a run of separation, the torsional stiffness, C, associated with interstrand winding of the two single strands comprising a separated site and the coefficient, K, of the quadratic free energy associated to residual linking. The experimental data used in this analysis are the locations and relative amounts of strand separation occurring in the pBR322 DNA molecule and the measured residual linking, both evaluated over a range of negative linking differences. The analytic method used treats strand separation as a heteropolymeric, co-operative, two-state transition to a torsionally deformable alternative conformation, which takes place in a circular DNA molecule constrained by the constancy of its linking number. The values determined for these parameters under the experimental conditions (T = 310 K, pH = 7.0, monovalent cation concentration = 0.01 M) are a = 10.84(+/- 0.2) kcal/mol, C = 2.5(+/- 0.3) x 10(-13) erg/rad2 and K = 2350(+/- 80) RT/N, where N is the molecular length in base-pairs. In order to assess the accuracy of the author's theoretical methods, these free energy parameters are incorporated into the analysis of superhelical strand separation in different molecules and under other conditions than those used in their evaluation. First, the temperature dependence of transition is treated, then superhelical strand separation is analyzed in a series of DNA molecules having systematic sequence modifications, and the results of these theoretical analyses are compared with those from experiments. In all molecules, transition is predicted in the range of linking differences where it is seen experimentally. Moreover, it occurs at the specific sequence locations that the analysis predicts, and with approximately the predicted relative amounts of transition at each location. The known sensitivities of this transition to changes of temperature and to small sequence modifications are predicted in a quantitatively precise manner by the theoretical results. The demonstrated high-level precision of these theoretical methods provides a tool for the screening of DNA sequences for sites susceptible to superhelical strand separation, some of which may have regulatory or other biological significance.