Biphasic helix-coil transition of the ethidium bromide-poly (dA-dT) and the propidium diiodide - poly (dA-dT) complexes. Stabilization of base-pair regions centered about the intercalation site

Modulation of the Antiviral Activity of Poly (A-U) by Ethidium Bromide and Propidium Iodide

The role of ethidium bromide (EB) and propidium iodide (PI) in modulating the antiviral and interferon-inducing activities of poly(adenylate-uridylate) (poly (A-U)) was examined using the human foreskin fibroblast-vesicular stomatitis virus (HSF-VSV) bioassay system in which the concentration of poly (A-U) was fixed at 0.05 mM or 0.2 mM while the EB or PI concentration was varied to produce variable EB (or PI)/ribonucleotide ratios ranging from 1:16 to 2:1. EB, PI and poly (A-U) tested individually were not efficacious antiviral agents. When poly (A-U) was combined with the ethidium bromide or propidium iodide the antiviral activity was potentiated 15- to 22-fold at EB (or PI)/ribonucleotide ratios in the region of 1/4. The interferon-inducing activity of the EB (or PI)/poly (A-U) combinations were equal to the sum of the interferon-inducing activity of the poly (A-U) and the EB or (PI). These results indicate that the EB and PI potentiate the antiviral activity of the poly (A-U) without superinduction of interferon. The direct viral inactivation study demonstrated that EB, PI, poly (A-U) and the EB (or PI)/poly (A-U) combinations did not inactivate the VSV at concentrations near the 50% viral inhibitory dose.

RNA–Intercalating Agent Interactions: in vitro Antiviral Activity Studies

Twenty intercalating agents were tested to examine the effects of intercalating dye-induced perturbations upon the antiviral activity of poly (adenylate–uridylate) [poly (A-U)]. Neither poly (A-U) alone nor each intercalative dye was an efficacious antiviral agent. When poly (A-U) was combined with major groove intercalating dyes (acridine orange or proflavine), no synergism was observed. When poly (A-U) was combined with minor groove intercalating dyes [ethidium (EB), propidium (PI), adriamycin (ADR) or daunomycin (DMN)] or minor/major groove intercalating dyes [9-aminoacridine (9-AA), N2-methyl-9-hydroxy-ellipticine (NMHE) or N2,N6-dimethyl-9-hydroxy-ellipticine (DMHE)] the 50% effective doses (ED50) of the poly (A-U), 9-AA, ADR, DMHE, DMN, EB, NMHE and PI decreased 18-, 22-, 60-, 274-, 61-, 154-, 113- and 299-fold, respectively. When poly (A-U) was combined individually with 11 dyes whose mode of intercalation was not known, the ED50 of ametantrone (HAQ), chloroquine (CHL), mitoxantrone (DHAQ) and quinine (QUI) decreased 125-, 65-, 251- and 32-fold, respectively. These results suggest that the four dyes may intercalate into poly (A-U) from the minor groove. Ten (ADR, CHL, DMN, DHAQ, DMHE, EB, HAQ, NMHE, PI, QUI) of the 20 dyes evaluated exhibited significant synergism with poly (A-U), as quantified by the fractional inhibitory concentration index. Interferon (IFN) neutralization assays demonstrated that the IFN-inducing capability of the dye/poly (A-U) combinations approximated the sum of the capabilities of the poly (A-U) and the dyes employed. These results suggest that the majority of the dyes tested potentiate the antiviral activity of poly (A-U) without affecting the amount of IFN induced.

Capillary electrophoretic separation of binaphthyl enantiomers with two polymeric chiral surfactants: 1H-nuclear magnetic resonance and fluorescence spectroscopy study

The use of the water-soluble polymeric chiral surfactants (PCS), sodium N-undecanoyl-L-valinate (poly-L-SUV) and sodium undecanoyl-L-isoleucinate (poly-L-SUI) as buffer additives in electrokinetic chromatography (EKC) afforded the separation of racemic mixtures of 2,2'-dihydroxy-1,1'-binaphthyl (BOH) and 1,1'-binaphthyl-2,2'-diyl hydrogen phosphate (BNP). The apparent binding constants of the PCS to the enantiomers of BNP and BOH were obtained through 1H-nuclear magnetic resonance (1H-NMR) titrations and fluorescence spectroscopy, respectively. The 1H-NMR titration studies show that the BNP enantiomers are localized in the hydrophobic micellar pockets of PCS and form complexes of a 1:1 stoichiometry. The binding constants of PCS of BOH were determined from a Benesi-Hildebrand treatment of the fluorescence data. The EKC data corroborate those of the binding constants, supporting the formation of inclusion complexes. A model rationalizing the chiral discrimination of the enantiomers of BNP is proposed based on the intermolecular interactions observed in 1H-NMR data.

Enthalpy-entropy compensations in drug-DNA binding studies

We present a comparative study of calorimetrically derived thermodynamic profiles for the binding of a series of drugs with selected DNA host duplexes. We use these data to demonstrate that comparisons between complete thermodynamic profiles (delta G zero, delta H zero, delta S zero, delta Cp) are required before drug binding can be used as a probe of DNA conformation, since enthalpy-entropy compensations can cause two drug-DNA binding events to exhibit similar binding free energies (delta G zero) despite being driven by entirely different thermodynamic forces (delta H zero, delta S zero). In this work, we employ a combination of spectroscopic and calorimetric techniques to characterize thermodynamically the DNA binding of netropsin and distamycin (two minor groove-directed ligands), ethidium (an intercalator), and daunomycin (a combined intercalator/groove binder). Our free energy data (delta G zero) show that each drug exhibits similar binding affinities at 25 degrees C for the alternating copolymer duplex poly[d(A-T)].poly[d(A-T)] and for the homopolymer duplex poly(dA).poly(dT). However, our calorimetric measurements reveal that the nature of the thermodynamic forces (delta H zero, delta S zero) that drive drug binding to these two host duplexes at 25 degrees C are entirely different, despite similar binding free energies (delta G zero) and similar salt dependencies (lnK/ln[Na+]). Specifically, the 25 degrees C binding of all four drugs to the alternating copolymer poly[d(A-T)].poly[d(A-T)] is overwhelmingly enthalpy driven, whereas the corresponding binding of each drug to the homopolymer duplex poly(dA).poly(dT) is overwhelmingly entropy driven. Thus, the similar binding free energies (delta G zero) we measure for complexation of each drug with poly[d(A-T)].poly[d(A-T)] and poly(dA).poly(dT) result from compensating changes in the enthalpy and entropy terms. Comparison with the thermodynamic profiles for the complexation of these drug molecules to other DNA host duplexes at 25 degrees C reveals that the binding of each is strongly enthalpy driven, except when the poly(dA).poly(dT) homopolymer serves as the host duplex. This comparison allows us to conclude that poly[d(A-T)].poly[d(A-T)] behaves thermodynamically as the more "normal" host duplex toward drug binding, whereas the entropy-driven binding to the poly(dA).poly(dT) duplex represents "aberrant" behavior. Furthermore, since each of the four drugs exhibits different modes of DNA binding, we conclude that the observed entropy-driven behavior for binding to poly(dA).poly(dT) reflects an intrinsic property of the homopolymer duplex that is perturbed in a common manner upon ligation rather than a common property of all four binding ligands. To rationalize the large positive entropy changes that drive drug complexation with poly(dA).poly(dT) duplex, we propose a model that emphasizes binding-induced perturbations of the more highly hydrated, altered B conformation of the homopolymer. Our results suggest that an aberrant thermodynamic binding profile may reflect an unusual DNA conformation in the host duplex. However, before such a conclusion can be reached, complete thermodynamic binding profiles must be examined, since enthalpy-entropy compensations can cause two binding events to exhibit similar binding constants even when they are driven by very different thermodynamic forces.

The thermodynamics of drug-DNA interactions: ethidium bromide and propidium iodide

We report the first calorimetrically-derived characterization of the thermodynamics of ethidium bromide (EB) and propidium iodide (PI) binding to a series of nucleic acid host duplexes. Our spectroscopic and calorimetric measurements yield the following results: 1) At low salt (16mM Na+) and 25 degrees C. PI binds more strongly than EB to a given host duplex. The magnitude of this PI preference depends only marginally on base sequence, with AT base pairs showing a greater PI preference than GC base pairs. 2) The enhanced binding of PI relative to EB at low salt and 25 degrees C reflects a more favorable entropic driving force for PI binding. 3) The PI binding preference diminishes at higher salt concentrations (216mM). In other words, the binding preference is electrostatic in origin. 4) The salt dependence of the binding constants (delta lnKb/delta ln[Na+]) reveal that PI binds as a dication while EB binds as a monocation. 5) PI and EB both exhibit impressive enthalpy-entropy compensations when they bind to the deoxy homopolymers poly dA.poly dT and poly dA.poly dU. We have observed a similar enthalpy-entropy compensation for netropsin binding to the poly dA.poly dT homopolymer duplex. We therefore conclude that the compensation phenomenon is an intrinsic property of the host duplex rather than reflecting a property of the binding ligand. 6) When either PI or EB bind to the corresponding ribo homopolymer (poly rA.poy rU) we do not observe the enthalpy-entropy compensation that characterizes the binding to the deoxy homopolymer. 7) EB and PI both bind more strongly to poly d(AT).poly d(AT) than to poly d(AU).poly d(AU). Specifically, the absence of the thymine methyl group in poly d(AU).poly d(AU) reduces the binding constant of both drugs by a factor of four. This reduction in binding is due to a less favorable entropy change. In this paper we present and discuss possible molecular origins for our observed thermodynamic and extra-thermodynamic data. In particular, we evoke solvent effects involving both the drugs and the host duplexes when we propose molecular interpretations which are consistent with our thermodynamic data.

Interaction between enzyme-generated triplet carbonyls and molecules intercalated into DNA

The phosphorescence from enzyme-generated and -protected triplet acetone is very efficiently quenched by dyes intercalated into DNA. The process is unlikely to be due to energy transfer and is tentatively ascribed to electron transfer occurring within the DNA helix complex with the acting enzyme. This quenching markedly protects DNA from breaks induced by triplet acetone. In the case of some barely emissive enzyme-generated triplet carbonyl species, it is possible to detect a weak emission resulting from the interaction with dye X DNA; this emission may be associated with back electron transfer.

Substituent effects on the binding of ethidium and its derivatives to natural DNA

The binding of eight ethidium derivatives to short (approximately 35 base-pair), random sequence DNA has been investigated using 1H-NMR. At 35 degrees C, all drugs cause upfield shifts of the DNA imino proton resonances characteristic of intercalative binding to DNA, but the line shapes vary significantly with the nature of the drug. The results confirm our previous proposal that removal of the amino group at position-3, but not at position-8, on the parent ethidium shortens the lifetime of the intercalative state (less than 1-2 ms at 35 degrees C). These results suggest that hydrogen-bonding interactions with the 3-NH2 group are involved in stabilization of the drug-DNA complex or that changes in charge distribution that accompany removal of the 3-NH2 group reduce the complex stability. The magnitude of the shift of the drug-DNA spectra indicates a slight preference for binding of the drugs adjacent to G X C base-pairs.

Interaction of bleomycin A2 with poly(deoxyadenylylthymidylic acid). A proton nuclear magnetic resonance study of the influence of temperature, pH, and ionic strength

The binding of bleomycin A2 to poly(deoxyadenylylthymidylic acid) [poly(dA-dT)] has been monitored by proton nuclear magnetic resonance spectroscopy. This study includes an analysis of the effects of temperature, ionic strength, and pH. Sites of drug-nucleic acid interaction have been delineated on the basis of chemical shift perturbations of drug and nucleic acid resonances. The data indicate that the binding of the antibiotic occurs with partial intercalation of the aromatic bithiazole group and immobilization of the cationic dimethylsulfonium group. This complex dissociates as the nucleic acid is denatured to the single-stranded form. The absence of significant pH effects suggests that the N terminus of bleomycin A2, which contains the titratable groups, does not contribute to the interaction of the drug molecule with poly(dA-dT). The problems associated with assigning a specific geometry to the drug-nucleic acid complex are discussed.

Comparative binding of ethidium and three azido analogs to dinucleotides: affinity and intercalation geometry. A 1H NMR and visible spectroscopy study

Geometrical and thermodynamic information has been obtained from theoretical analysis of both visible and 1H-NMR spectroscopic binding isotherms of ethidium and three photoactivable derivatives (8-azido-ethidium, 3-azido-ethidium and 3,8-diazido-ethidium) to self-complementary ribodinucleosides. The following results have been obtained. 1. Interaction with pyrimidine(3-5')purine sequences is well accounted for by multicomponent equilibria involving self-association of the dyes in oligomers, formation of 1:1 and 2:1 (nucleoside:dye) complexes. This model provided evidence for intercalation of all dyes, though with weaker affinity in the case of diazido-ethidium (2 X 10(6) M-2 vs 6 X 10(7) M-2). Moreover 3-azido-ethidium was shown to intercalate into cytidylyl(3'-5')guanosine (CpG) with its phenyl group lying in the major groove of the minihelix. This geometry is inverted with respect to that of all other compounds. It should be emphasized that visible and 1H-NMR techniques independently provided similar results (intercalation, affinity constants) therefore supporting this stepwise model. 2. Interaction of all dyes with purine(3'-5')pyrimidine sequences is not intercalative, even at low temperature (4 degrees C), but is well described by self-association of the dyes and formation of 1:1 (nucleoside:dye) complexes. Regarding the reversible DNA intercalation process, these studies show that 8-azido-ethidium is the only photoactivatable derivative which behaves exactly as ethidium. Therefore 8-azido-ethidium can be used as a covalent probe to investigate the DNA-related cytotoxic effects of ethidium.

1H NMR study of an ethidium dimer poly(dA-dT) complex: evidence of a transition between bis and monointercalation

Comparative 1H NMR and optical studies of the interaction between poly(dA-dT), ethidium bromide (Et) and ethidium dimer (Et2) in 0.7 M NaCl are reported as a function of the temperature. Denaturation of the complexes followed at both polynucleotide and drug levels leads to a biphasic melting process for poly(dA-dT) complexed with ethidium dimer (t1/2 = 75 degrees C; 93 degrees C) but a monophasic one in poly(dA-dT): ethidium bromide complex (t1/2 = 74 degrees C). In both cases drug signals exhibit monophasic thermal dependence (Et = 81 degrees C; Et2 = 95 degrees C). Evidence is presented showing that the ethidium dimer bisintercalates into poly(dA-dT) in high salt, based on the observation that i) dimer and monomer ring protons exhibit similar upfield shifts upon DNA binding, ii) upfield shifts of DNA sugar protons are twice as large with the dimer than with ethidium bromide. Comparison between native DNA fraction and bound drug fraction indicates that ethidium covers, n = 2.5-3 base pairs. The dimer bisintercalates and covers, n = 5.7 base pairs when the helix fraction is high but as the number of available sites decreases the binding mode changes and the drug monointercalates (n = 2.9).

Binding of ethidium derivatives to natural DNA: a 300 MHz 1H NMR study

The binding of three ethidium derivatives, ethidium (1), des-3-amino ethidium (2) and des-8-amino ethidium (3), to short (approximately 35 base pairs), random sequence DNA has been investigated using 300 MHz proton NMR. At 35 degrees C all three drugs cause upfield shifts of the resonances from the exchangeable imino protons, as expected for intercalative binding to DNA. However, the lineshapes vary significantly with the nature of the drug. The temperature dependence of the spectra of the DNA shows that differences between spectra observed at 35 degrees C with ethidium and with des-3-amino ethidium are primarily due to differences in the drug binding kinetics rather than to differences in mode of binding. Removal of the amino group at position 3, but not at position 8, on the parent ethidium shortens the lifetime of the intercalative state; this implies that the 3-NH2 group is involved in stabilization of the drug-DNA complex. Analysis of the drug-DNA spectra indicates that there is a preference for binding of the drugs adjacent to G.C base pairs.

Hydrogen bonding, overlap geometry, and sequence specificity in anthracycline antitumor antibiotic.DNA complexes in solution

We have deduced structural aspects of the intercalation complex of the anthracycline antitumor antibiotic daunomycin and its analogs with the synthetic DNA poly(dA-dT) by 1H and 31P NMR in high-salt solution. We demonstrate that the base pairs are intact at the antibiotic binding site and that the anthracycline phenolic hydroxyls form intramolecular hydrogen bonds with the quinone carbonyls and are shielded from solvent in the intercalation complex. The complexation shifts of the exchangeable phenolic and nonexchangeable aromatic protons demonstrate that rings B and C of the anthracycline chromophore overlap with adjacent base pairs, while anthracycline ring D passes right through the intercalation site in the complex. We observe two resolved 31P resonances attributable to the dA-dT and dT-dA phosphodiester linkages in the phosphorus spectra of the neighbor-exclusion daunomycin.poly(dA-dT) complex. This suggests that the anthracycline antitumor antibiotic exhibits a sequence specificity in its intercalation complex with alternating purine-pyrimidine synthetic DNAs in solution. These conclusions on hydrogen bonding and overlap geometry at the intercalation site and sequence specificity for the daunomycin.poly(dA-dT) complex in solution are in agreement with the structure of the daunomycin.dC-dG-dT-dA-dC-dG hexanucleotide duplex crystalline complex at atomic resolution published recently [Quigley, G. J., Wang, A. H.-J., Ughetto, G., van der Marel, G., van Boom, J. H. & Rich, A. (1980) Proc. Natl. Acad. Sci. USA 77, 7204-7208].

Anthracycline antitumor antibiotic nucleic-acid interactions. Structural aspects of the daunomycin poly(dA-dT) complex in solution

The helix-to-coil transition of the synthetic DNA poly(dA-dT) in the presence of the anthracycline antitumor antibiotic daunomycin has been investigated by high-resolution proton nuclear magnetic resonance (NMR) spectrocopy in 1 M salt solution. The dissociation of the complex, containing molar ratios of phosphate to daunomycin (Pi/drug) of 50, 25, 9 and 5, with increasing temperature can be monitored independently at the nucleic acid and the antibiotic resonances under conditions of fast exchange. The antibiotic complex formation shifts suggest that either ring B and/or C of the intercalated anthracycline chromophore of daunomycin overlaps with adjacent nucleic acid base pairs. Ultraviolet/visible melting studies of daunomycin complexes with a series of synthetic DNAs substituted with halogen atoms (Br, I) at position 5 of the pyrimidine ring suggest that intercalation of the antibiotic into poly(dA-dU) is not perturbed by bulky substituents at this position. A comparison of the melting curves for the daunomycin . poly(dA-dT) complex with an analog of the antibiotic where the NH3 + group is replaced by dimethylglycine demonstrates the important contributions of electrostatic interactions between the amino sugar and backbone phosphates to the stability of the complex in low salt solution. The ultraviolet/visible and NMR studies monitor biphasic melting transitions at the nucleic acid markers in the daunomycin . poly(dA-dT) complexes, Pi/drug = 50--9, so that antibiotic-free base-pair regions and those centered about bound daunomycin can be independently studied at the synthetic DNA level in solution.

Synthesis, DNA-binding and biological activity of a double intercalating analog of ethidium bromide

A bis-phenanthridinium salt has been synthesized and its DNA-binding studied. Evidence provided by UV and CD spectra, by thermal denaturation profiles and by equilibrium dialysis of the drug-DNA complex lead to the conclusion that both phenanthridine moieties intercalate in the helix. The double intercalator appears to be less potent than ethidium chloride as an inhibitor of nucleic acid synthesis in cultured L1210 cells, though it is more potent than a monomeric analog. The low potency may be due to a low cell influx rate.

The interaction of daunomycin with polydeoxynucleotides

The ability of daunomycin to bind to various DNA polymers has been sutided by thermal denaturation, spectrophotometric analysis and inhibition of the polymerisation reactions catalysed by Escherichia coli DNA polymerase I and rat liver DNA polymerase alpha. The quantitative binding measurements revealed that the antibiotic binds tightly to all synthetic polydeoxynucleotides studied. The results demonstrated that daunomycin can bind with equal affinity to dG . dC or dA . dT basepaired sequences. However, the number of binding sites per nucleotide for poly(dA) . poly(dT) is significantly lower than that found for poly(dA-dT) . poly(dA-dT), thus indicating an appreciable preference of the drug for the alternating copolymer. The inactivation of the template properties of the synthetic DNA polymers in the DNA polymerase system is consistent with their daunomycin binding ability. However, a lack of correlation was observed between the drug binding ability of different DNA polymers and the binding-induced stabilisation of the double helix to heat denaturation.