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PubMed1975

Triplet state population study in relation to the aggregation of proflavine in frozen solutions.

The evolution of the proflavine triplet state population with the extent of aggregation is examines, by ESRmeasurements, as a function of organic solvents and mineral salts, well known for their ability to influence the aggregation process. The intensity of the triplet state population has also been investigated as a function of pH. The insertion of aromatic molecules like DNA's nucleotides between dye molecules is shown to increase the intensity of the triplet state. It is put forward that the observed triplet state is characteristic of the singly protonated proflavine which seems to be the active species in in vivo experiments.

Acridines↗
PubMed1976

[Photosensitization of consitutents of nucleic acids by proflavine. Mechanism of formation of hydrogen addition radicals in frozen aquenous solutions (author's transl)].

It is shown that the insertion of nucleotides between proflavine molecules is favourable to photosensitization. Furthermore (1) each molecule of proflavine gives at the most one free radical in the substrate, (2) the chromophore is largely restored when oxygen is not present, (3) superoxide radicals are observed in the presence of oxygen, and (4) formyl radicals are detected. The scheme elaborated for the mechanism gives an explanation for all these observations.

Acridines↗
PubMed1977

[Hydrogen-adduct radicals in thymidine and thymidine 5'-monophosphate photosensitized by proflavin. Protection by sulfur compounds (author's transl)].

At pH values 5 and 9, the influence of cysteine, cystine, 3-mercaptopropionic acid and S-methylcysteine on the induction of H-adduct radicals in thymidine and thymidine 5'-monophosphate photosensitized by proflavin is investigated. The results obtained indicate that efficient protection is given when the electrostatic interactions between the charged groups of the molecules present allow the close proximity of a thiol or a disulfide bridge and the proflavin - DNAs complex constituent. The scheme proposed for the mechanism involves the capture by the protector of an electron or a proton, indispensable intermediates in the formation of the H-adduct radicals.

Acridines↗
PubMed1977

Fluorescence decay and quantum yield characteristics of acridine orange and proflavine bound to DNA.

Fluorescence properties (quantum yield, decay curve, lifetime and polarization) of acridine orange and proflavine bound to DNA were examined as a function of nucleotide to dye (P/D) ratio. First, mean fluorescence lifetimes were determined by the phase-shift measurements. The lifetime and quantum yield of acridine orange increased in a parallel fashion with increasing P/D ratio. There was no parallel relation between the lifetime and quantum yield for proflavine; the lifetime showed a minimum around P/D equals 10...

Acridines↗
PubMed2002

Synthesis and DNA interaction of a mixed proflavine-phenanthroline Tröger base.

We report the synthesis of an asymmetric Tröger base containing the two well characterised DNA binding chromophores, proflavine and phenanthroline. The mode of interaction of the hybrid molecule was investigated by circular and linear dichroism experiments and a biochemical assay using DNA topoisomerase I. The data are compatible with a model in which the proflavine moiety intercalates between DNA base pairs and the phenanthroline ring occupies the DNA groove. DNase I cleavage experiments were carried out to investigate the sequence preference of the hybrid ligand and a well resolved footprint was detected at a site encompassing two adjacent 5'-GTC.5-GAC triplets. The sequence preference of the asymmetric molecule is compared to that of the symmetric analogues.

Azocines↗
PubMed1986

Proflavin binding to poly[d(A-T)] and poly[d(A-br5U)]: triplet state and temperature-jump kinetics.

The delayed fluorescence properties of proflavin have been exploited in studies of the excited-state binding kinetics of the dye to poly[d(A-T)] and its brominated analogue poly[d(A-br5U)] at room temperature and pH 7. The two analyzed luminescence decay times of the DNA-dye complex are dependent on the total nucleic acid concentration. This dependence is shown to reflect a temporal coupling of the intrinsic delayed emission decay rates with the dynamic chemical kinetic binding processes in the excited state. Temperature-jump kinetic studies conducted on the brominated polymer and corresponding information on poly[d(A-T)] from a previous study [Ramstein, J., Ehrenberg, M., & Rigler, R. (1980) Biochemistry 19, 3938-3948] provide complementary information about the ground state. In the ground state, the poly[d(A-T)]-proflavin complex has one chemical relaxation time, which reaches a plateau at high DNA concentrations. The brominated DNA-dye complex exhibits two relaxation times: a faster relaxation mode that behaves similarly to that for the unhalogenated DNA and a slower relaxation mode that is apparent at high DNA concentrations. The ground-state kinetic data are analyzed in terms of two alternative models incorporating series and parallel reaction schemes. The former consists of two sequential binding steps--a fast bimolecular process followed by a monomolecular step--while the latter consists of two coupled bimolecular steps. A similar analysis for the excited-state data yields reasonable kinetic constants only for the series model, which, in accordance with previous proposals for acridine intercalators, consists of a fast outside binding step followed by intercalation of the dye. A comparison of the ground- and excited-state kinetic parameters reveals that the external binding process is much stronger and the intercalation is much weaker in the excited state. That the excited-state data are only consistent with the series model suggests that delayed luminescence studies may provide a general tool for distinguishing between the two kinetic mechanisms. In particular, we demonstrate the use of delayed luminescence spectroscopy as a tool for probing dynamic DNA-ligand interactions in solution.

Acridines↗
PubMed1980

Fluorescence relaxation of proflavin-deoxyribonucleic acid interaction. Kinetic properties of a base-specific reaction.

The kinetics of proflavin binding to Micrococcus lysodeicticus deoxyribonucleic acid (DNA [(G-C) content 72%], to Bacillus megaterium DNA [(A-T) content 70%], and to the polydeoxyribonucleotides poly[d(G-C)] and poly[d(A-T)] was studied with fluorescence temperature-jump methods. Poly[d(A-T)] binds proflavin in a two-step reaction with a preequilibrium. Poly[d(G-C)] is characterized by a bimolecular reaction. The binding of acridines to natural DNAs is shown to be characterized by different types of sites whose properties depend on the base composition. The sites have considerable enthalpic differences which result in exchange of dye molecules between them when the temperature is changed. Also, on natural DNAs A-T base pairs are associated with a rapidly equilibrating external complex which is absent or much weaker for G-C base pairs.

Acridines↗
PubMed1976

Influence of electric dichroism on the temperature-jump relaxation study of proflavine-DNA complexes.

The temperature-jump relaxation kinetics of proflavine-DNA complexes has been reinvestigated with a standard apparatus equipped for absorption detection of plane-polarized light in order to discriminate between chemical relaxation and transient orientation effects. Under low ionic strength conditions (0.015 M Na+), these effects may represent the major contribution to the signal when the T-jump apparatus is used without a polarizer. They have been improperly assigned to chemical relaxation in previous work. The actual relaxation times are smaller than 30 musec at 10 degrees C. Under medium ionic strength conditions (0.2 M Na+) it is shown that: (i) the "instantaneous" change of transmission reported in earlier work (Li, H. J., and Crothers, D. M. (1969), J. Mol. Biol. 39, 461-477; Schmechel, D. E. V., and Crothers, D. M. (1971), Biopolymers 10, 465-480) is due to orientation effects; (ii) an intermediate exists whose absorption spectrum resembles somewhat that of proflavine aggregates on a linear polyanion; (iii) the rate constants for outside binding may be significantly larger than previously reported. The new kinetic data are consistent with a modified mechanism derived from equilibrium studies (Ramstein, J., Hogrel, J. F., Dourlent, M., Leng, M., an Hélène, C. 1973), in Dynamic Aspects of Conformation Changes in Biological Macromolecules, Sadron, C., Ed., Dordrecht, Holland, Reidel Publisher, pp 333-347; Dourlent, M., and Hogrel, J. F. (1976), Biopolymers (in press)), but, however, do not unambiguously prove it. From these studies, it is inferred that orientation effects can perturb relaxation data on systems containing linear polymers in many cases.

Acridines↗
PubMed2006

Ethidium and proflavine binding to a 2',5'-linked RNA duplex.

Despite over 40 years of physical investigations, fundamental questions persist regarding the energetics of RNA and DNA intercalation. The dramatic unwinding of a nucleic acid duplex upon intercalation immediately suggests that the nucleic acid backbone should play a significant role in dictating the free energy of intercalation. However, the contribution of the backbone to intercalation free energy is difficult to appreciate given the intertwined energetics associated with intercalation (e.g., pi-pi stacking and solvent effects). Fluorescence titrations were used to determine the association constants of two known intercalators, proflavine and ethidium, for duplex 2',5'-linked RNA. Proflavine was found to bind 2',5' RNA with an association constant 25-fold greater than that measured for standard, 3',5'-linked RNA. In contrast, ethidium binds 2',5' RNA less favorably than standard RNA.

Binding Sites↗
PubMed1986

Frameshift mutations produced by proflavin in bacteriophage T4: specificity within a hotspot.

Frameshift mutations were induced by proflavin in the rIIB gene of bacteriophage T4. rIIB DNA from each of 48 independent frameshifts was inserted into M13mp8 and sequenced. Two-thirds of the frameshifts (33/48) lie contiguous to one another in 10 base pairs of the rIIB sequence. This hotspot differs markedly from previously characterized mutagen-induced frameshift hotspots. Distinctive features of the hotspot include the absence of locally repetitive sequences, particularly G X C runs, and the fact that many different sequence changes are induced within the hotspot sequence at appreciable frequencies. Among the 33 mutants at the hotspot, 8 distinguishable DNA sequence changes were seen. All of the mutations were deletions of a single base or duplications of one or more bases. Duplications were more frequent than deletions. The patterns of the base sequence changes suggest that two specific phosphodiester bonds within the hotspot sequence are sites at which proflavin-induced mutation is initiated.

Acridines↗
PubMed1990

Inhibition of replicative DNA synthesis and induction of DNA repair in human fibroblasts by the intercalating drugs proflavine and 9-aminoacridine.

The induction of unscheduled DNA synthesis (UDS) and the alteration of semiconservative DNA replication by the structurally related intercalating agents proflavine and 9-aminoacridine were studied in MRC-5 human fibroblasts in culture. Autoradiographic determinations of both parameters were carried out simultaneously in the same culture specimens. Proflavine affected DNA synthesis, but did not elicit any UDS. 9-Aminoacridine inhibited DNA synthesis only at the highest concentration and caused UDS to a low but significant extent. These results suggest that the ability to induce UDS is not a general property of the intercalating agents and that the alterations of the DNA structure, typical of the "pure" intercalative process, are not handled by pathways involving unscheduled synthesis.

Aminacrine↗
PubMed1984

Flow cytometric analysis of proflavine uptake into normal rat hepatocytes and cells arising during AAF-induced hepatocarcinogenesis.

The uptake of the fluorescent drug proflavine was measured in suspensions of hepatocytes from normal and carcinogen (2-acetylaminofluorine, AAF)-fed rats by flow cytometry. Drug uptake into hepatocytes from carcinogen-fed animals was consistently lower than that into hepatocytes from normal animals. Isolated nuclei, prepared from the livers of normal and AAF-fed rats showed similar proflavine uptake. Drug uptake into hepatocytes from AAF-fed animals, however, was increased by prior exposure to a metabolic inhibitor. Thus, differences in drug uptake may reflect changes in the cell membrane, together with an alteration in the metabolic integrity of the cells. The uptake of drug in hepatocytes from AAF-fed rats was uniformly low within each cell preparation. However, drug uptake varied not only between tumours arising in the livers of these animals but also within each tumour cell preparation. This study indicates that flow cytometry can provide an effective means for analysing drug uptake into cell populations arising during hepatocarcinogenesis.

2-Acetylaminofluorene↗
PubMed1988

A molecular model for proflavine-DNA intercalation.

A molecular model has been derived for the intercalation of proflavine into the CpG site of the decamer duplex of d(GATACGATAC). The starting geometry of the intercalation site was taken from previous crystallographic studies on the d(CpG)-proflavine complex, and molecular mechanics used to obtain a stereochemically acceptable structure. This has widened grooves compared to standard A- or B- double helices, as well as distinct conformational, roll, twist and tilt features.

Acridines↗
PubMed1977

Proflavine sensitivity of RNA processing in isolated nuclei.

The intercalating agent proflavine inhibits the processing and subsequent release of preformed messenger RNA and ribosomal RNA from isolated liver nuclei to surrogate cytoplasm. The direct effect of proflavine on these processes, as monitored in a reconstituted cell-free system, supports the theory that base-paired segments (i.e. hairpin loops) in the precursor RNA's are involved as recognition sites in nuclear RNA processing.

Acridines↗
PubMed1978

A 1:2 crystalline complex of ApA:proflavine: a model for binding to single-stranded regions in RNA.

The structure of a 1"2 complex of adenylyl-(3',5')-adenosine phosphate and proflavine hemisulfate has been determined using the methods of x-ray crystallography. Since the ApA does not form a mini double helix, it may serve as a model for the interaction of planar molecules with single stranded nucleic acids. The dinucleotide adopts an extended conformation with the adenines in adjacent molecules forming base pairs. A most unusual feature of the molecule is that it does not obey the "rigid nucleotide" concept although none of the torsion angles occur in energetically unfavourable regions. This is most probably due to the strong interactions between the proflavine and the oligonucleotide.

Acridines↗
PubMed1981

Theoretical studies of the structure and energies of base-paired nucleotides and the dissociation kinetics of a proflavine-dinucleotide complex.

We presented calculations of base-paired dinucleoside phosphates and hexanucleoside pentaphosphates of varying compositions. Complete energy minimizations were performed for (a) the ten base-pair combinations of dinucleoside phosphates, starting from a B-DNA conformation, (b) six hexanucleoside pentaphosphates--base-paired CGCGCG, GCGCGC, G6-C6, TATATA, ATATAT, and A6-T6--starting with a B-DNA geometry, and (c) the four hexanucleoside pentaphosphates that have alternating pyrimidine-purine sequences, starting with a Z-DNA geometry. In addition, we studied the proflavine-base-paired CpG complex, using both complete energy minimization and energetic constraints to force the drug to dissociate from the dinucleoside phosphate. In many of these calculations, we examined the dependence of the calculated energies and structures on the potential function, focusing mainly on the effect of nonbonded potentials, the effective dielectric constant, and the role of counterions. These calculations allow us to explain why pur-(3',5')-pyr sequence isomers are more stable than pyr-(3'-5')-pur isomers. Both base-base and base-backbone energies are important in this differentiation, with the former being mainly van der Waals attraction and the latter mainly electrostatic energies. The calculations also allow us to understand the differences in double helical stabilities found by Wells et al. These differences, caused by electrostatic interactions between those bases not Watson-Crick hydrogen bonded, allow us to explain the following experimental data: poly(dG-dC) melts 12 degrees C higher than poly dG-poly dC, poly(dA-dT) melts 6 degrees C lower than poly dA-poly dT, and poly(dA-dG)-poly(dC-dT) melts 6 degrees C lower than poly(dA-dC)-poly(dT-dG). These results have interesting implications for drug binding: they imply that simple intercalators, such as ethidium, will exhibit a greater affinity for hetero- than for homopolymers and that this preference will be greater in the AT polymers than it is in the GC polymers. Our calculations allow us to explain the fact that Z-DNA is more stable than B-DNA under high salt conditions and to suggest some sequence dependence for the Z to B transition. We found that the activation energy for proflavine dissociating from dCpG is almost equal to the dissociation energy.

Acridines↗
PubMedDate not supplied

[Thermodynamic analysis of the interaction of the acridine dye proflavin with deoxytetranucleotides with various base sequences from (1)H-NMR data].

Temperature dependences of proton chemical shifts of the molecules in aqueous solutions of proflavine with deoxytetraribonucleoside triphosphates of different base sequence--5'-d(CGCG), 5'-d(GCGC), 5'-d(ACGT) and 5'-d(AGCT) have been studied by 500 MHz NMR spectroscopy. Methods of calculation of thermodynamical parameters of complex formation, giving an opportunity to differentiate the contributions of the reactions leading to the formation of different types of complexes in conditions of the composite equilibrium in solution, have been suggested. Enthalpies and entropies of the reactions of 1:1, 2:1, 1:2, 2:2 complexes formation between proflavine and tetranucleotides have been determined. Comparative analysis of the calculated thermodynamical parameters has been made and assumptions about the nature of intermolecular interactions responsible for the formation of dye complexes with different tetranucleotides have been proposed.

Base Sequence↗
PubMedDate not supplied

[Interaction of proflavin with deoxytetraribonucleoside triphosphate 5'-d(ApGpCpT): thermodynamic analysis from (1)H NMR data].

Temperature relationships of chemical shifts of protons of proflavin mixed with deoxytetraribonucleoside triphosphate 5'-d(ApGpCpT) in water solution were investigated on impulse NMR spectrometer (500 MHz). Procedure is suggested for calculating values of mole fractions of various associates in solution as a function against temperature. Free energies of Gibbs, entalpy and entropy were determined in the reactions of complex formation 1:1, 1:2, 2:1 of proflavin with tetranucleotide. The results point to a significant role of hydrophobic interactions during the formation of dye--tetramere duplex complexes.

Magnetic Resonance Spectroscopy↗