Interaction of polynuclear aromatic hydrocarbons, 4-nitroquinoline 1-oxides, and various dyes with DNA

Substituted Aromatic-Facilitated Dissemination of Mobile Antibiotic Resistance Genes via an Antihydrolysis Mechanism Across an Extracellular Polymeric Substance Permeable Barrier

Mobile antibiotic resistance genes (ARGs) in environmental systems may pose a threat to public health. The coexisting substituted aromatic pollutants may help the ARGs cross the extracellular polymeric substance (EPS) permeable barrier into the interior of cells, facilitating ARG dissemination, but the mechanism is still unknown. Here, we demonstrated that a specific antihydrolysis mechanism of mobile plasmid in the extracellular matrix makes a greater contribution to this facilitated dissemination. Specifically, fluorescence microtitration with a Tb³⁺-labeled pUC19 plasmid was used to study the formation of substituted aromatic-plasmid complexes associated with ARG dissemination. Manipulations of the endA gene and an EPS confirmed that these forming complexes antagonize the EPS-mediated hydrolysis of the plasmid. Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and computational chemistry demonstrated that substituents alter the polarity of aromatic molecules, making the carbon at the 6-position of 1,3-dichlorobenzene as well as the labile protons (-NH₂/-OH) of m-phenylenediamine, aniline, and 2-naphthol interact with the deprotonated hydroxy group of the phosphate (P-O···H-C/N/O), mainly via hydrogen bonds. Linear correlations among ARG disseminations, association constants, and bonding energies highlight the quantitative dependency of ARG proliferation on a combination of functionalities templated by d-ribose-phosphate.

Linear dichroism of DNA: Characterization of the orientation distribution function caused by hydrodynamic shear

Linear dichroism provides information on the orientation of chromophores part of, or bound to, an orientable molecule such as DNA. For molecular alignment induced by hydrodynamic shear, the principal axes orthogonal to the direction of alignment are not equivalent. Thus, the magnitude of the flow-induced change in absorption for light polarized parallel to the direction of flow can be more than a factor of two greater than the corresponding change for light polarized perpendicular to both that direction and the shear axis. The ratio of the two flow-induced changes in absorption, the dichroic increment ratio, is characterized using the orthogonal orientation model, which assumes that each absorbing unit is aligned parallel to one of the principal axes of the apparatus. The absorption of the alienable molecules is characterized by components parallel and perpendicular to the orientable axis of the molecule. The dichroic increment ratio indicates that for the alignment of DNA in rectangular flow cells, average alignment is not uniaxial, but for higher shear, as produced in a Couette cell, it can be. The results from the simple model are identical to tensor models for typical experimental configurations. Approaches for measuring the dichroic increment ratio with modern dichrometers are discussed.

Photobiological activity of Ru(II) dyads based on (pyren-1-yl)ethynyl derivatives of 1,10-phenanthroline

Several mononuclear Ru(II) dyads possessing 1,10-phenanthroline-appended pyrenylethynylene ligands were synthesized, characterized, and evaluated for their potential in photobiological applications such as photodynamic therapy (PDT). These complexes interact with DNA via intercalation and photocleave DNA in vitro at submicromolar concentrations when irradiated with visible light (lambda(irr) > or = 400 nm). Such properties are remarkably sensitive to the position of the ethynylpyrenyl substituent on the 1,10-phenanthroline ring, with 3-substitution showing the strongest binding under all conditions and causing the most deleterious DNA damage. Both dyads photocleave DNA under hypoxic conditions, and this photoactivity translates well to cytotoxicity and photocytotoxicity models using human leukemia cells, where the 5- and 3-substituted dyads show photocytotoxicity at 5-10 microM and 10-20 microM, respectively, with minimal, or essentially no, dark toxicity at these concentrations. This lack of dark cytotoxicity at concentrations where significant photoactivity is observed emphasizes that agents with strong intercalating units, previously thought to be too toxic for phototherapeutic applications, should not be excluded from the arsenal of potential photochemotherapeutic agents under investigation.

Synthesis and biophysical studies of coronene functionalized 2'-amino-LNA: a novel class of fluorescent nucleic acids

Incorporation of 2'-N-(coronen-1-yl)methyl-2'-amino-LNA monomer X or 2'-N-4-(coronen-1-yl)-4-oxobutanoyl-2'-amino-LNA monomer Y into short DNA strands induces high binding affinity toward DNA or RNA and a marked red-shift in steady-state fluorescence emission upon hybridization to cDNA or RNA.

The induction of SOS function in Escherichia coli K-12/PQ37 by 4-nitroquinoline oxide (4-NQO) and fecapentaenes-12 and -14 is bile salt sensitive: implications for colon carcinogenesis

The response of Escherichia coli to genotoxic agents involves the triggering of a complex system of genes known as the SOS response. In E. coli PQ37, a test organism used for the assessment of genotoxicity, lacZ, the beta-galactosidase gene is placed under the control of sfiA, one of the SOS genes through an operon fusion. The induction of beta-galactosidase activity, when the organism is exposed to genotoxic agents, is an indirect measure of the genotoxic activity of the test compound. Incubation of E. coli PQ37 with either 4-nitroquinoline oxide (4-NQO) or one of the fecal mutagens, fecapentaene-12 or -14 (F-12 or F-14) in the presence of sodium taurocholate or sodium deoxycholate resulted in a significant enhancement of induction of beta-galactosidase activity. The molecular mechanisms of 4-NQO-induced mutagenesis in E. coli are similar to those of the effects of UV light in which both replication-dependent and repair-dependent pathways of mutagenesis exist. Since E. coli PQ37 is excision-repair-deficient, alternate pathways are involved in this system. Bile salts by themselves do not trigger the SOS response, and hence their role in enhancing the SOS-inducing potency of mutagens may involve the potentiation of the cleavage-inactivation of lexA (repressor of SOS) by the protein product of the SOS-controlled gene, recA. The potentiating effect of bile salts on the fecal mutagens, F-12 and F-14, has implications in their suspected role in colon carcinogenesis associated with high-fat, low-fiber diets.

Polycyclic aromatic hydrocarbons physically intercalate into duplex regions of denatured DNA

We have investigated the physical binding of pyrene and benzo[a]pyrene derivatives to denatured DNA. These compounds exhibit a red shift in their absorbance spectra of 9 nm when bound to denatured calf thymus DNA, compared to a shift of 10 nm when binding occurs to native DNA. Fluorescence from the hydrocarbons is severely quenched when bound to both native and denatured DNA. Increasing sodium ion concentration decreases binding of neutral polycyclic aromatic hydrocarbons to native DNA and increases binding to denatured DNA. The direct relationship between binding to denatured DNA and salt concentration appears to be a general property of neutral polycyclic aromatic hydrocarbons. Absorption measurements at 260 nm were used to determine the duplex content of denatured DNA. When calculated on the basis of duplex binding sites, equilibrium constants for binding of 7,8,9,10-tetrahydroxy-7,8,9,10-tetrahydro-benzo[a]pyrene to denatured DNA are an order of magnitude larger than for binding to native DNA. The effect of salt on the binding constant was used to calculate the sodium ion release per bound ligand, which was 0.36 for both native and denatured DNA. Increasing salt concentration increases the duplex content of denatured DNA, and it appears that physical binding of polycyclic aromatic hydrocarbons consists of intercalation into these sites.

A comparison of the intercalative binding of non-reactive benzo[a]pyrene metabolites and metabolite model compounds to DNA

The reversible DNA physical binding of a series of non-reactive metabolites and metabolite model compounds derived from benzo[a]pyrene (BP) has been examined in UV absorption and in fluorescence emission and fluorescence lifetime studies. Members of this series have steric and pi electronic properties similar to the highly carcinogenic metabolite trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) and the less potent metabolite 4,5-epoxy-4,5-dihydrobenzo(a)pyrene (4,5-BPE). The molecules examined are trans-7,8-dihydroxy-7,8-dihydrobenzo[a]-pyrene (7,8-di(OH)H2BP), 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (tetrol) 7,8,9,10-tetrahydrobenzo[a]pyrene (7,8,9,10-H4BP), pyrene, trans-4,5-dihydroxy-4,5-dihydrobenzo[a]pyrene (4,5-di(OH)H2BP) and 4,5-dihydrobenzo[a]pyrene (4,5-H2BP). In 15% methanol at 23 degrees C the intercalation binding constants of the molecules studied lie in the range 0.79-6.1 X 10(3) M-1. Of all the molecules examined the proximate carcinogen 7,8-di(OH)-H2BP is the best intercalating agent. The proximate carcinogen has a binding constant which in UV absorption studies is found to be 2.8-6.0 times greater than that of the other hydroxylated metabolites. Intercalation is the major mode of binding for 7,8-di(OH)H2BP and accounts for more than 95% of the total binding. Details concerning the specific role of physical bonding in BP carcinogenesis remain to be elucidated. However, the present studies demonstrate that the reversible binding constants for BP metabolites are of the same magnitude as reversible binding constants which arise from naturally occurring base-base hydrogen bonding and pi stacking interactions in DNA. Furthermore, previous autoradiographic studies indicate that in human skin fibroblasts incubated in BP, pooling of the unmetabolized hydrocarbons occurs at the nucleus. The high affinity of 7,8-di(OH)H2BP for DNA may play a role in similarly elevating in vivo nuclear concentrations of the non-reactive proximate carcinogen.

Pyrene as a sensitive probe for DNA conformational changes due to protonation

Planar pyrene molecules can acquire optical activity upon binding to the disymmetric environment of duplex DNA. Positive induced Cotton effects are observed for pyrene in basic and neutral DNA solutions but revert to strongly negative CD bands in moderately acidic solutions. pH titrations indicate that this change over is strongly cooperative until acid denaturation sets in. The negative induced CD for pyrene results from its binding to a protonated duplex state which shows a striking 40 degrees C decrease in the melting temperature from its neutral counterpart with 0.18 M NaCl. Further studies with synthetic polynucleotides reveal that pyrene strongly prefers the guanine containing sequences in general and dG-dC (and/or dC-dG) sequence(s) in particular for this protonated duplex state, in distinct contrast to the dA-dT (and/or dT-dA) sequence specificity in the neutral solutions. The observed pyrene CD sign reversal upon protonation is thus the manifestation of DNA conformational change and the accompanied alteration in base sequence specificity.

Binding of pyrene to DNA, base sequence specificity and its implication

Solubilization as well as spectral studies of pyrene in natural DNA and synthetic deoxypolynucleotide solutions at neutral pH reveal at least two binding modes. Sites I are predominant in native DNA and in poly(dA-dT): poly(dA-dT) whereas sites II are found with denatured DNA and other polynucleotides such as poly(dA):poly(dT) and three different types of guanine containing copolymers which solubilize pyrene to a lesser extent. Spectral comparison with the covalent adducts of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10- tetrahydro-benzo(a)pyrene (anti-BPDE) and the physical complexes of its tetraols lead to the suggestion of a base sequence specific binding model for this carcinogenic metabolite to account for the puzzling fact that although its physical binding is predominantly intercalative, the covalent adducts appear not to be intercalated. It is speculated that in neutral solutions, intercalation may have little, if any, to do with the chemical lesion of this metabolite to the guanine base of the DNA and may, on the contrary, provide an efficient pathway for detoxification.

Electro-optical fluorescence studies on the DNA binding of medically active drugs

By measuring the transient changes in each of the polarized components of fluorescence during the application of a pulsed electric field to a solution of macromolecules, a method has been developed for evaluating the binding characteristics of fluorescent chemotherapeutic agents to DNA. It is shown that whereas quinacrine and berberine intercalate the DNA helix, hydroxystilbamidine does not. Furthermore, measurements on both the native and the diol-epoxide forms of benzo(a)pyrene show that the former is consistent with an intercalation type of binding, whilst the latter appears to be more inclined to the major DNA axis and may possibly be associated with the external helical grooves. The significance of these findings is discussed.

A simple method for studying the solubilization of polycyclic aromatic hydrocarbons in DNA solutions

A simple method for detecting the amount of a polycyclic aromatic hydrocarbon (PAH) solubilized in DNA solutions is described. This method takes advantage of the fact that sodium dodecyl sulfate (SDS) induces dissociation of PAH from DNA, and the greatly enhanced solubility of PAH in SDS solution makes possible the direct preparation of a standard solution for the extinction coefficient determination. The ability to make direct comparison between the spectroscopic characteristics before and after dissociation is accomplished by utilizing a tandem cuvette. The usefulness of this technique is then demonstrated by applying it to solubilization studies of pyrene in native and denatured DNA solutions of varying sodium chloride concentrations as well as in deoxymononucleotide solutions. Binding constants are estimated and the solubility data for pyrene in the DNA solutions are interpreted in terms of the binding abilities of intercalative versus external sites and the effect of salt. The mononucleotide results suggest a binding preference of pyrene to purine bases. It was observed that the binding constant of mononucleotide to pyrene is an order of magnitude lower than that of single-stranded DNA, which in turn is an order of magnitude smaller than that of duplex DNA.

Probing the microenvironment of benzo[a]pyrene diol epoxide-DNA adducts by triplet excited state quenching methods

Triplet flash photolysis techniques, coupled with quenching of the triplets by molecular oxygen, are utilized as probes of the microenvironment of polycyclic aromatic molecules bound covalently and non-covalently to DNA. The triplet-oxygen quenching properties of the following adducts in aqueous solutions at 25 +/- 1 degrees C were investigated: covalent adducts derived from the reaction of (+/-)-7 beta,8 alpha-dihydroxy-9 alpha,10 alpha-epoxy-7,8,9, 10-tetrahydrobenzo[a]pyrene (BaPDE) and of (+/-)-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BaPE) with DNA, and non-covalent intercalation complexes of acridine orange (AO) and DNA. In all cases the quenching follows the Stern-Volmer quenching law with a quenching constant of KTO2 approximately equal to 10(9) M-1 X S-1 for the covalent BaPDE-DNA and BaPE-DNA complexes in aqueous solution. This value of KTO2 is characteristic of free molecules (not bound to DNA) and indicates that the pyrene chromophore is totally accessible to oxygen, and is thus not located at an intercalation-type of binding site in these covalent adducts. In contrast, the AO-DNA complexes are characterized by values of KTO2 approximately equal to 10(8) M-1 X S-1 indicating that the intercalated AO molecules are about ten times less accessible to molecular oxygen than free AO molecules. The KTO2 values for the covalent BaPDE-DNA and BaPE-DNA adducts decrease when the DNA concentration is increased in the 1 X 10(-4)-3 X 10(-3) M range (expressed in nucleotide concentration). This effect is attributed to intermolecular DNA-DNA interactions in which segments of adjacent DNA molecules tend to cover the pyrene chromophores on other strands, thus decreasing their accessibility to oxygen. In contrast the values of KTO2 for the non-covalent AO-DNA intercalation complexes are independent of DNA concentration, as expected for interior binding sites.

Molecular models of induced DNA premutational damage and mutational pathways for the carcinogen 4-nitroquinoline 1-oxide and its metabolites

The carcinogen 4-nitroquinoline 1-oxide (4NQO) and its metabolites undergo intercalative or covalent binding with DNA. Recent evidence indicates that the latter binding pattern is probably facilitated by an initial weaker intercalative interaction that can align potentially reactive sites on a 4NQO-metabolite and adjacent stacked bases. In the present study, we have proposed numerous possible covalent reaction products between 4NQO and its metabolites with DNA mini-helices based on chemical properties and key 'short-contacts' after energy-minimization in 21 different intercalative-like complexes. It is known from numerous experimental studies that 90% of the quinoline-bound DNAs in vivo involve guanine with the remaining 10% apparently involving adenine residues. The results of the present study suggest that this trend is not due to the greater affinity of the quinolines for guanine, but instead results from secondary processes involving the preferential formation of apurinic sites at aralkyl-adenine residues over that of aralkyl-guanine residues. In addition, observed mutational patterns can be rationalized in terms of the proposed reaction-products. The role of DNA repair mechanisms in the removal and correction of the different proposed reaction products are discussed. The binding pattern of several other aromatic carcinogens are similar to those depicted in the present work for the 4NQO-metabolites; hence the present study may be of some general significance.

Nucleic acid base and carcinogen metabolite specificities during intercalative interactions between DNA and 4-nitroquinoline 1-oxide

Intercalation of the carcinogen 4-nitroquinoline 1-oxide (4-NQO) or its metabolic intermediate forms, probably precedes the covalent bond formation of the ultimate carcinogenic form with DNA. A 'complete' empirical-potential energy description of the base-sequence and metabolite specificities of the 4-NQO intercalation process is presented in this work. The important force and structural interaction components are depicted via decomposed energy functions. Energy-minimized intercalated complexes are presented and indicate several interesting characteristics. It is clear that the various intercalated quinoline-metabolites do not generally enter into 'strictly' parallel-planar stacked orientations (unlike the structurally rigid ethidium-intercalated complexes). Intercalation is energetically permitted for six of seven quinoline-metabolites (QMS) studied, although, intercalation into to Pyr(3'-5')Pur sequences is preferred over Pur(3'-5'1Pyr sequences. The three quinoline-metabolites that are more energetically favoured to undergo intercalation than the parent form are also known to enter into the greatest amount of covalent interactions with DNA and its constituents. Thus the present work further suggests the existence of a two-step binding mechanism: intercalation followed by covalent reaction.

Solubilization of 6-oxybenzo(a)pyrene radical by caffeine and DNA as studied by magnetic resonance. Observation of intermolecular charge transfer

Crystals of 6-oxybenzo(a)pyrene free radical, formed chemically from the hydroxy derivative of the carcinogen benzo(a)pyrene, can be solubilized in aqueous solutions of DNA and of caffeine. ESR spectral evidence indicate that the radicals exist as dispersed monomers associated with DNA and with caffeine. Comparison of NMR spin-lattice and spin-spin relaxation times in the protons of caffeine has given direct evidence that a part of the unpaired electron (at least 10(-4)) is transferred from the radical to the associated caffeine molecule. Simple consideration of Mulliken's charge transfer theory, however, leads to the conclusion that the intermolecular charge transfer is not likely to be a major source of stabilization energy of the complex.

Interactions of 4-nitroquinoline 1-oxide with four deoxyribonucleotides

The interactions of 4-nitroquinoline 1-oxide (NQO) with the four 5'-deoxyribonucleotides were probed using absorption spectra of the charge transfer bands and 1H and 13C nuclear magnetic resonance (NMR) spectra of nucleotide-NQO mixtures. Spectral data yielded equilibrium constants (K(dpG:NQO) = 16 M-1, K(dpA:NQO) = 12 M-1, K(dpT:NQO) = K(dpC:NQO) = 4 M-1) which suggest the preference of NQO for the guanine residue in a DNA. This is in agreement with the data of Okano, T., et al. [(1969) Gann 60, 295]. From 13C and 1H NMR data on nucleosides, a structure for the dpG:NQO complex is proposed.

Flow dichroism, flow polarized fluorescence and viscosity of the DNA acridine complexes

The strong binding of various acridine dyes to DNA has been studied by the measurements of flow dichroism, flow polarized fluorescence and viscosity. Negative flow dichroism and percentage change in polarized fluorescence intensity show that intercalated dye molecules are oriented rather perpendicularly to the main axis of the DNA helix, like base pairs. On the other hand, viscosity measurements show that the increase of the contour length of DNA depends on the dye structure, being much smaller in the case of dyes with bulky substituents compared to that of the other dyes. This may be attributed to the formation of the outside bound complex. Further, the introduction of bulk substituents to the acridine ring leads to a little smaller values of the reduced dichroism and intensity change of polarized fluorescence. The results may be qualitatively understood if we assume that the outside bound dye lies in the groove of the DNA helix and the plane of the dye tilts from the perpendicular direction relative to the main axis of the helix.

Physico-chemical study of the complexes of "33258 Hoechst" with DNA and nucleohistone

The degree of binding of "33258 Hoechst" to DNA and nucleohistone has been determined by equilibrium dialysis and the properties of the complexes have been followed by different optical and electro-optical methods, after determining the orientation of the main transition moments within the dye molecule. The binding isotherm was found composed of a Langmuir-type and of a strongly cooperative component. The existence of two bound species yielded a continuous variation of most of the properties of the complexes studied as the amount of binding increased, while the hydrodynamic properties of the macromolecules were not affected. At low binding, the strongly bound dye molecules appeared to bind to highly fluorescent sites with their long axis oriented at 45 degree to the helix axis. As the binding proceeds, less fluorescent sites are cooperatively occupied and the inclination of these ligand molecules becomes closer to that of the base planes. These results are compatible with the formation of two external complexes with the double helical structure.

Analyses of differential sensitivities of synchronized HeLa S3 cells to radiations and chemical carcinogens during the cell cycle. III. 4-Nitroquinoline 1-oxide and its derivatives

Sensitivity to the chemical carcinogens 4-nitroquinoline 1-oxide (4-NQO) and 4-hydroxyaminoquinoline I-oxide (4-HAQO), during the cell cycle of synchronized HeLa S3 cells, decreases from the late S to the early G2 phases. Cells in other phases are relatively sensitive to both carcinogens. [3-H]4-NQO and [ 3-H]4-HAQO seem to be bound preferably more with cellular DNA of the mitotic phase to the middle of the S phase than with that of the late S phase in which the cells are rather insensitive to these carcinogens. However, we found no significant difference in the excision rates of these carcinogens from the DNA of HeLa S3 cells through the cell cycle. These findings indicate that the cyclic variation of 4-NQO and 4-HAQO cell survivals during the cell cycle may be due to the differences in the amounts of 4-NQO and 4-HAQO bound with cellular DNA.