9-aminoacridine inhibits the B-Z transition of poly(dA-dT).

9-Aminoacridine is the parent compound of a family of pharmacologically active model substances that bind to DNA through intercalation between base pairs. In the present study we show that 9-aminoacridine inhibits the B-to-Z isomerization of poly(dA-dT) in conditions that otherwise cause it to occur (5 M NaCl and 123 mM Ni(ClO4)2). Higher concentrations of Ni(ClO4)2 (155 mM) are able to induce the Z-form due to the disruption of the drug-polynucleotide interaction by the metal ion. Additionally, the dye reverses the Z-form in certain conditions. Thus, the data from this study indicate that 9-aminoacridine binds preferentially to the B-form of poly(dA-dT).     

Acridine dimers: influence of the intercalating ring and of the linking-chain nature on the equilibrium and kinetic DNA-binding parameters

The rigidity of the linking chain of bifunctional intercalators in the ditercalinium series was shown to be critical for antitumor activity. In order to study the influence of the rigidity of the linking chain on the DNA-binding properties of DNA bifunctional intercalators, fluorescent 9-aminoacridine and 2-methoxy-6-chloro-9-aminoacridine analogues with chains of variable rigidity were synthesized. 1H-NMR studies show that the conformation of 9-aminoacridine dimers is almost independent of the nature of the linking chain. A strong self-stacking of the aromatic rings of the 2-methoxy-6-chloro-9-aminoacridine is observed for dimers with flexible chains but not for those with rigid chains. All the dimers having a linking chain long enough to bisintercalate in DNA according to the excluded site model are indeed bisintercalators. The kinetic association constant of all monomers and dimers for poly[d(A-T)].poly[d(A-T)] are in the same range (2-4 x 10(7) M-1 s-1). The large increase of DNA binding affinity observed for the dimers is always associated with the expected decrease of the dissociation rate constant. The effect of chain rigidity and pH on the calf thymus DNA binding of 9-aminoacridine and 2-methoxy-6-chloro-9-aminoacridine dimers is quite different. In the series of 9-aminoacridine the pKa of the dimers remains high and therefore no difference of DNA-binding affinity is observed between pH 5 and 7.4. The rigidity of the linking chain does not significantly alter the DNA-binding affinity. In the 2-methoxy-6-chloro-9-aminoacridine series, the pKa of all dimers became smaller than the physiological pH and a dramatic decrease of DNA-binding affinity is observed when the pH is increased from pH 5 to 7.4. This decrease appears significantly smaller for dimers with rigid chains. A similar dramatic decrease of binding affinity at pH 7.4 is not observed for poly[d(A-T)].poly[d(A-T)]. This factor makes these dimers strongly specific for the alternating polymer at pH 7.4.     

Molecular mechanisms of chemical mutagenesis: 9-aminoacridine inhibits DNA replication in vitro by destabilizing the DNA growing point and interacting with the DNA polymerase

9-Aminoacridine was found to inhibit dNTP incorporation into DNA homopolymer duplexes by phage T4 DNA polymerase in vitro. Systematic variation of the molar ratio of 9-aminoacridine to DNA, to DNA polymerase, and to DNA precursors demonstrated that this inhibition at 9-aminoacridine concentrations below 10 microM was mainly due to interaction of 9-aminoacridine with the DNA and suggested that the basis for the preferential inhibition of incorrect precursor incorporation was destabilization of the DNA growing point. Consistent with destabilization, 9-aminoacridine stimulated the hydrolysis of correctly base paired DNA by the 3'-5' exonuclease activity of phage T4 DNA polymerase. This is the first indication to my knowledge that an intercalating dye destabilizes the DNA growing point, whereas it raises the overall Tm of the DNA. At 9-aminoacridine concentrations above 10 microM overall incorporation of dNTPs was inhibited by 9-aminoacridine interaction with the DNA polymerase. A possible explanation for the induction of both deletion and addition frameshift mutations by 9-aminoacridine during DNA biosynthesis is discussed in light of growing-point destabilization.     

The binding of 9-aminoacridine to calf thymus DNA in aqueous solution. Electronic spectral studies

Absorption, circular dichroism and steady-state fluorescence spectra were determined of 9-aminoacridine solutions in the presence of DNA at an ionic strength of 0.001 mol dm-3. Up to a dye/DNA phosphorus ratio of about 0.2 the results are fully consistent with the requirements and predictions of a binding model already shown to apply to the binding of other aminoacridines to DNA. The apparently anomalous spectroscopic behaviour of the 9-aminoacridine/DNA system compared with proflavine/DNA, for example, can be satisfactorily explained from a consideration of the magnitudes of exciton interactions between dyes bound to DNA.     

Evidence for heterogeneity in DNA-associated solvent mobility from acridine phosphorescence spectra

The mobility of solvent associated with native DNA in comparison with that of the bulk solvent is monitored from the temperature-dependent red shift in the phosphorescence spectra of acridines bound to DNA and free in glycol–buffer mixtures. Over the temperature range for which the red shift occurs the phosphorescence decay changes with emission wavelength, indicating the time-dependent nature of the process. Moreover, at these temperatures, emission anisotropy measurements establish that motions of the dye itself are not involved. Correspondence between perturbations to the solvent that influence the temperature at which the red shift occurs for free acridine with those for the DNA-bound dye confirm that “bound solvent” is responsible for the spectral changes. For the DNA-bound acridines the extent of the red shift is smaller and the midpoint T_1/2 of the transition is warmer. The reduction in the red shift reveals that the bound dye is less exposed to solvent and varies as 9-aminoacridine < acridine orange ～ proflavin, i.e., 9-amino-acridine is less exposed to solvent. On the other hand, the warmer T_1/2 indicates that DNA-associated solvent is considerably less mobile than bulk solvent. T_1/2 varies for proflavin bound to DNA, poly[d(AT)], poly[d(GC)], and poly(dG): poly(dC), and for proflavin, acridine orange, and 9-aminoacrine bound to DNA. These observations suggest that there is a heterogeneity in the mobility of DNA-associated solvent.     

Interaction of proflavine and 9-aminoacridine with DNA at temperatures below and above the melting temperature

The influence of temperature on the binding of 9-aminoacridine and of proflavine to E. coli DNA in 10^?3M NaCl solution has been determined by a spectrophotometric technique. The inadequacy of the expression normally used for the determination of the extent of binding is discussed with reference to measurements at temperatures above which dissociation of the double helix occurs. A method of determining the relative extents of binding to native and denatured DNA at elevated temperatures is described.     

Linear dichroism studies of nucleic acids. III. Reduced dichoism curves of DNA in ethanol–water and in poly(vinyl alcohol) films

The uv linear dichroism of calf thylus DNA has been studied at different degrees of orientation both in flow-oriented ethanol–water solutions and in a stretched aqueous host of poly(vinyl alcohol) (PVA). The reduced dichroism (LD^R) curves in the region 250–290 nm for DNA in PVA films at 75 and 100% relative humidity (r.h.) are in fair agreement with the curves calculated for the A- and B-forms of DNA, based on the fiber structures and the π-π* transitions of the free bases. This suggests that DNA adopts its A and B conformations in PVA at 75 and 100% r.h. In ethanol, on the other hand, a deviation from the A-form spectrum shows that the conformation of DNA in the solution can differ from the fiber structure. At shorter wavelenghts, a positive contribution to LD^R is explained in terms of an out-of-plane polarized n-π* transition.     

Induction of deletion and insertion mutations by 9-aminoacridine. An in vitro model

The ability of 9-aminoacridine to induce mutagenic lesions during DNA replication in vitro was investigated. The ampicillinase gene of pBR322 was replicated in vitro in the presence of 9-aminoacridine. Transfection of the replicated DNA into Escherichia coli gave Amps mutants. Determination of the base changes in 76 of these mutants indicated that the spectrum of mutations induced by 9-aminoacridine was consistent with its action in vivo. Both large (407-base) and small (1- and 2-base) deletions were induced at repetitive sequences. The frequency of deletion mutations depended on the identity of the base deleted and sequences surrounding the deletions. The characteristics of the frameshift mutations induced were consistent with the interactions of 9-aminoacridine with DNA. These results establish that 9-aminoacridine can induce frameshift mutations during the replication process and provide an in vitro model of frameshift induction for mechanistic studies.     

The interaction of an anti-tumour platinum complex with DNA.

The interaction of the anti-tumour active cis platinum (II) complexes with DNA has been investigated using dichloro(ethylenediamine)platinum(II) and E. coli DNA. Equilibrium dialysis studies indicate that Pt(en)Cl2 binds reversibly to DNA to a saturation value of 0.57 Pt: P, which is consistent with the platinum being bound both monofunctionally and bifunctionally. Pt(en)Cl2 inhibits the intercalation of 9-aminoacridine (9AA) by cross-linking the bases of the double helix, but at no stage does all the bound platinum cross-link. It is suggested that this inhibition of intercalation is due to intrastrand cross-linking.     

Photochemical cleavage of DNA by nitrobenzamides linked to 9-aminoacridine

Nitrobenzamido ligands linked to the DNA intercalator 9-aminoacridine via poly(methylene) chains induce single-strand nicks in DNA upon irradiation with long-wavelength ultraviolet light (lambda greater than or equal to 300 nm). Optimal photocleavage activity was found for the reagent 9-[[6-(4-nitrobenzamido)hexyl]amino]-acridine. Removal of the acridinyl ligand or changing the position of the nitro group from the 4- to the 2-position caused a 10-fold decrease in photocleavage efficiency, whereas a change to the 3-position caused a 30-fold reduction. The DNA cleavage was 5-fold enhanced by subsequent piperidine treatment and showed some sequence dependency with predominant cleavage at G and T residues. Furthermore, significant differences in cleavage preference were observed when the poly(methylene) linker length was changed.     

The inhibition of ribonucleic acid polymerase by acridines

1. The aminoacridines, proflavine (3,6-diaminoacridine) and 9-aminoacridine, and a hydrogenated derivative, 9-amino-1,2,3,4-tetrahydroacridine, were shown to inhibit in vitro the DNA-primed RNA polymerase of Escherichia coli. The inhibition is strong with both proflavine and 9-aminoacridine, but weak with 9-amino-1,2,3,4-tetrahydroacridine. 2. The extent to which the three acridines bind to calf-thymus DNA in the enzyme medium was studied spectrophotometrically. The extent of binding decreases in the order: proflavine, 9-aminoacridine, 9-amino-1,2,3,4-tetrahydroacridine. Some evidence was also obtained for interaction between the nucleoside triphosphate substrates and proflavine or 9-aminoacridine; no such interaction was detectable with 9-amino-1,2,3,4-tetrahydroacridine. 3. Although the amount of acridine bound to DNA increases with increasing inhibition, a stage is reached where an increase in acridine concentration still causes an increase in inhibition, with practically no increase in the amount bound to DNA. 4. Plots of reciprocal rates against the reciprocal of DNA concentration were linear and had a common intercept when proflavine or 9-aminoacridine was present. Similar relations were obtained when the reciprocal concentration of nucleoside triphosphates was plotted. The observations are interpreted kinetically in terms of a competitive inhibition of the enzyme by proflavine or 9-aminoacridine and of a kinetic role for the DNA analogous to ;activation'. 5. This suggests that inhibitory acridine molecules can occupy the sites on the RNA polymerase that are specific for binding the nucleoside triphosphate substrate or the bases of the DNA, when these become accessible during the copying process.     

9-Aminoacridine, a fluorescent probe of the thiamine carrier in yeast cells

The uptake of 9-aminoacridine is studied in the yeast Saccharomyces cerevisiae by fluorescence and absorbance measurements of the dye. Uptake of the dye proceeds via two pathways. One pathway consists of a diffusion of the non-protonated form. At high pH (7.5) this pathway is the predominant one, and the dye distributes between the cell inner and the medium according to the ratio of the proton concentrations in the two compartments. In other words, at high pH 9-aminoacridine behaves as a probe of the H⁺ gradient across the yeast cell membrane. At low external pH (4.5) a second pathway is involved. Much greater accumulation ratios for the dye are observed than can be accounted for by the H⁺ gradient across the membrane. The transport system predominantly responsible for the great accumulation of the dye appears to be inducible, to require metabolic energy and to be saturable. This transport system is competitively inhibited by thiamine, and also by dibenzyldimethylammonium and thiaminedisulfide, two specific inhibitors of the thiamine carrier in the yeast. On the other hand, the thiamine uptake by the yeast cells is competitively inhibited by 9-aminoacridine. In addition, uptake of 9-aminoacridine is greatly reduced in the thiamine transport-negative mutant of S. cerevisiae, PT-R2. It is concluded that at low pH 9-aminoacridine is taken up by yeast via the thiamine carrier of the cell and that, consequently, the dye may be applied as a probe of this transport system.     

Oligodeoxynucleotides covalently linked to intercalating dyes as base sequence-specific ligands. Influence of dye attachment site.

New molecules with high and specific affinity for nucleic acid base sequences have been synthesized. They involve an oligodeoxynucleotide covalently attached to an intercalating dye. Visible absorption spectroscopy and fluorescence have been used to investigate the binding of poly(rA) to octadeoxythymidylates substituted by a 9-aminoacridine derivative in different positions along the oligonucleotide chain. The 9-amino group of the acridine dye was linked through a polymethylene bridge to the 3''-phosphate, the 5''-phosphate, the fourth internucleotidic phosphate or to both the 3''- and 5''-phosphates. Different interactions of the acridine dye were exhibited by these different substituted oligodeoxynucleotides when they bind to poly(rA). The interaction was shown to be specific for adenine-containing polynucleotides. The stability of these complexes was compared with that of oligodeoxynucleotides substituted by an alkyl group on the 3''-phosphate. The increase in stability due to the presence of the intercalating dye has been determined from the comparison of melting temperatures. These results are discussed with respect to the strategy of synthesis of a new class of molecules with high affinity and high specificity for nucleic acid base sequences.     

Kinetic and hydrodynamic studies of the complex of proflavine with poly A·poly U

Relaxation kinetic experiments reveal general similarity between the mechanism of binding of proflavine to poly A·poly U and DNA. There are differences in detail, however. For example, the rate constants are roughly an order of magnitude smaller for the former, and the thermodynamic parameters of the individual steps are also different. The total heat and free energy for intercalation of free dye are quite similar in the two cases. As was the case with DNA, considerable dye (up to 25% of the bound form) is attached externally to the double helix, even in the strong binding region of the isotherm. Sedimentation measurements on small, rodlike fragments of poly A·poly U reveal a length increase on binding proflavine of a magnitude similar to that found with DNA. This length increase seems to become smaller under conditions (high temperature) where the relaxation measurements indicate a higher fraction of externally bound dye.     

Photodynamic activity of dyes with different DNA binding properties II. T4 phage inactivation.

The photosensitizing efficiency of six dyes--proflavine, 9-aminoacridine, ethidium bromide, thiopyronine, pyronine and acridine red--have been compared on the basis of the inactivation of sensitized T4 phage caused by light irradiation. This reaction was only measurable after diffusion of the dye through the phage capsid and was not observed in the presence of either chloroquine or quinacrine; it followed a single-hit kinetics as a function of the irradiation time. With each dye, a double reciprocal plot of the inactivation constant versus the dye concentration present gave rise to a linear relationship. From this relation, parameters were deduced which expressed the relative photosensitizing efficiencies. Dye-binding to the phages was measured and the proflavine-mediated inactivation appeared to be related to the amount of strongly bound molecules. Such a conclusion could not be reached in the case of 9-aminoacridine and ethidium bromide, which were much less efficient photosensitizers than proflavine, but which were also strongly bound to the phages. Thiopyronine was weakly bound to the phages; it had, however, the highest photosensitizing activity observed. These results indicate that various mechanisms are involved when the phage photosensitization is due to one dye or another.     

The sequence selectivity of DNA-targeted 9-aminoacridine cisplatin analogues in a telomere-containing DNA sequence

In this study, the detailed DNA sequence specificity of four acridine Pt complexes was examined and compared with that of cisplatin. The DNA sequence specificity was determined in a telomere-containing DNA sequence using a polymerase stop assay, with a fluorescent primer and an automated capillary DNA sequencer. The Pt compounds included an acridine intercalating moiety that was modified to give a 9-aminoacridine derivative, a 7-methoxy-9-aminoacridine derivative, a 7-fluoro-9-aminoacridine derivative and a 9-ethanolamine-acridine derivative. Compared with cisplatin, the DNA sequence specificity was most altered for the 7-methoxy-9-aminoacridine compound, followed by the 9-aminoacridine derivative, the 7-fluoro-9-aminoacridine compound and the 9-ethanolamine-acridine derivative. The DNA sequence selectivity for the four acridine Pt complexes was shifted away from runs of consecutive guanines towards single guanine bases, especially 5′-GA dinucleotides and sequences that contained 5′-CG. The sequence specificity was examined in telomeric and non-telomeric DNA sequences. Although it was found that telomeric DNA sequences were extensively damaged by the four acridine Pt complexes, there was no extra preference for telomeric sequences.     

Drug-DNA sequence-dependent interactions analysed by electric linear dichroism.

The interactions between 20 drugs and a variety of synthetic DNA polymers and natural DNAs were studied by electric linear dichroism (ELD). All compounds tested, including several clinically used antitumour agents, are thought to exert their biological activities mainly by virtue of their abilities to bind to DNA. The selected drugs include intercalating agents with fused and unfused aromatic structures and several groove binders. To examine the role of base composition and base sequence in the binding of these drugs to DNA, ELD experiments were carried out with natural DNAs of widely differing base composition as well as with polynucleotides containing defined alternating and non-alternating repeating sequences, poly(dA).poly(dT), poly(dA-dT).poly(dA-dT),poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC). Among intercalating agents, actinomycin D was found to be by far the most GC-selective. GC selectivity was also observed with an amsacrine-4-carboxamide derivative and to a lesser extent with methylene blue. In contrast, the binding of amsacrine and 9-aminoacridine was practically unaffected by varying the GC content of the DNAs. Ethidium bromide, proflavine, mitoxantrone, daunomycin and an ellipticine derivative were found to bind best to alternating purine-pyrimidine sequences regardless of their nature. ELD measurements provided evidence for non-specific intercalation of amiloride. A significant AT selectivity was observed with hycanthone and lucanthone. The triphenyl methane dye methyl green was found to exhibit positive and negative dichroism signals at AT and GC sites, respectively, showing that the mode of binding of a drug can change markedly with the DNA base composition. Among minor groove binders, the N-methylpyrrole carboxamide-containing antibiotics netropsin and distamycin bound to DNA with very pronounced AT specificity, as expected. More interestingly the dye Hoechst 33258, berenil and a thiazole-containing lexitropsin elicited negative reduced dichroism in the presence of GC-rich DNA which is totally inconsistent with a groove binding process. We postulate that these three drugs share with the trypanocide 4',6-diamidino-2-phenylindole (DAPI) the property of intercalating at GC-rich sites and binding to the minor groove of DNA at other sites. Replacement of guanines by inosines (i.e., removal of the protruding exocyclic C-2 amino group of guanine) restored minor groove binding of DAPI, Hoechst 33258 and berenil. Thus there are several cases where the mode of binding to DNA is directly dependent on the base composition of the polymer. Consequently the ELD technique appears uniquely valuable as a means of investigating the possibility of sequence-dependent recognition of DNA by drugs.     

On the triplet states of polynucleotide--acridine complexes. I. Triplet energy delocalization in the 9-aminoacridine-DNA complex

Phosphorescence and fluorescence from the dye in complexes of DNA with 9-amino-acridine and acridine orange in a glycerol-H₂O glass have been measured at 77°K. The dependence of the p/fratio for 9-aminoacridine on the exciting wavelength demonstrates triplet–triplet energy transfer from DNA to dye. The result provides evidence for π electron overlap between the dye and the bases of native DNA. The observation that the magnitude of the enhancement in ultraviolet-excited dye phosphorescence increases with the base to dye ratio indicates triplet delocalization in the polymer. Preliminary flash experiments provide evidence that this delocalization is not limited by slow diffusion of the triplet exciton. The inability to detect transfer on denaturation of the DNA illustrates the sensitivity of triplet–triplet energy transfer to the conformation of the macromolecular complex.     

Sodium-23 NMR spin-lattice relaxation rate studies of mono- and bis-intercalation in DNA

23Na spin-lattice relaxation rate (1/T1 = R1) measurements have been used to study the intercalation of a series of 9-aminoacridine derivatives in DNA. The 23Na relaxation rate is strongly dependent upon the amount of intercalator added to a sodium DNA solution. The results are analyzed by a combined use of the ion condensation theory and the quadrupolar relaxation theory of polyelectrolyte solutions. This interpretation shows that the major effect in lowering the relaxation rate by intercalation is not due to the release of sodium ions but is caused by a substantial decrease in the relaxation rate Rb for the remaining bound sodium ions. Likewise, titration of NaDNA solutions with MgCl2 shows that condensation of Mg2+ on the DNA double helix reduces Rb. A good agreement between experiment and theory is found if the average lengthening following intercalation of a 9-aminoacridine moiety is assumed to be approximately 2.7 A. The distinction between mono- and bis-intercalation is clearly indicated by the results. The two bis-intercalating drugs examined are found to bis-intercalate only up to r less than or equal to 0.02. For r greater than 0.02 the drugs apparently mono-intercalate.     

Use of 9-aminoacridine as a probe in a kinetic study of DNA-poly-L-lysine interaction

An attempt has been made to use a fluorescent dye as a probe in a kinetic study of DNA-poly-L-lysine interaction by the stopped-flow method. It is found that 9-aminoacridine is suitable for this purpose. The results have indicated that polylysine binds to DNA at least in two steps; a slow unimolecular process (τ ～ 2 msec) being preceded by a rapid bimolecular one (τ ? 1 msec). The usefulness of this method for the kinetic study of the interaction between DNA and basic polypeptides has been emphasized.