Intercalation of a Zn(II) complex containing ciprofloxacin drug between DNA base pairs

In this study, an attempt has been made to study the interaction of a Zn(II) complex containing an antibiotic drug, ciprofloxacin, with calf thymus DNA using spectroscopic methods. It was found that Zn(II) complex could bind with DNA via intercalation mode as evidenced by: hyperchromism in UV–Vis spectrum; these spectral characteristics suggest that the Zn(II) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. DNA binding constant (K_b = 1.4 × 10⁴ M^?1) from spectrophotometric studies of the interaction of Zn(II) complex with DNA is comparable to those of some DNA intercalative polypyridyl Ru(II) complexes 1.0 ?4.8 × 10⁴ M^?1. CD study showed stabilization of the right-handed B form of DNA in the presence of Zn(II) complex as observed for the classical intercalator methylene blue. Thermodynamic parameters (ΔH < 0 and ΔS < 0) indicated that hydrogen bond and Van der Waals play main roles in this binding prose. Competitive fluorimetric studies with methylene blue (MB) dye have shown that Zn(II) complex exhibits the ability of this complex to displace with DNA-MB, indicating that it binds to DNA in strong competition with MB for the intercalation.     

Interaction between tryptophan‐Sm(III) complex and DNA with the use of a acridine orange dye fluorophor probe

The interaction of the Trp–Sm(III) complex with herring sperm DNA (hs‐DNA) was investigated with the use of acridine orange (AO) dye as a spectral probe for UV‐vis spectrophotometry and fluorescence spectroscopy. The results showed that the both the Trp–Sm(III) complex and the AO molecule could intercalate into the double helix of the DNA. The Sm(III)–(Trp)₃ complex was stabilized by intercalation into the DNA with binding constants: K^?_25°C = 7.14 × 10⁵ L·mol^?1 and K^?_37°C = 5.28 × 10⁴ L·mol^?1, and it could displace the AO dye from the AO–DNA complex in a competitive reaction. Computation of the thermodynamic functions demonstrates that Δ_rH_m^? is the primary driving power of the interaction between the Sm(III)(Trp)₃ complex and the DNA. The results from Scatchard and viscometry methods suggested that the interaction mode between the Sm(III)(Trp)₃ complex and the hs‐DNA is groove binding and weak intercalation binding. Copyright © 2015 John Wiley & Sons, Ltd.     

86 Characterization and differentiation of binding modes of water-soluble porphyrins at complexation with DNA

The influence of water-soluble cationic meso-tetra-(4?N-oxyethylpyridyl)porphyrin (H₂TOEPyP4) and it’s metallocomplexes with Ni, Cu, Co, and Zn on hydrodynamic and spectral behavior of DNA solutions has been studied by UV/Vis absorption and viscosity measurement. It was shown that the presence of planar porphyrins such as H₂TOEPyP4, NiTOEPyP4, and СuTOEPyP4 leads to an increase in viscosity at relatively small concentrations, and then decrease to stable values. Such behavior is explained by intercalation of these porphyrins in DNA structure because the intercalation mode involves the insertion of a planar molecule between DNA base pairs which results in a decrease in the DNA helical twist and lengthening of the DNA. Further decrease of viscosity is explained by the saturation intercalation sites and occurs outside the binding mode. But, in the case of porphyrins with axial ligands such as CoTOEPyP4 and ZnTOEPyP4, the hydrodynamic parameters decrease, which is explained by self-stacking of these porphyrins in DNA surface. This data are proved by spectral measurements. The results obtained from titration experiments were used for calculation of binding parameters: the binding constant K _b and the number of binding sites per base pair n. Obtained data reveal that K _b varies between 3.4 and 5.4?×?10⁶?M^?1 for a planar porphyrins, a range typical for intercalation mode interactions, and 5.6?×?10⁵?M^?1 and 1.8?×?10⁶?M^?1 for axial porphyrins. In addition, the exclusion parameter n also testifies that at intercalation, (n～2) the adjacent base pairs are removed to place the planar molecules, and for outside binders to pack on the surface needs too few places (n～0.5–1). It is apparent that the binding is somewhat stronger at intercalation. The viscometric and spectrophotometric measurements are in good agreement.     

Intercalative DNA Binding of Model Compounds Derived From Metabolites of 7, 12-Dimethylbenz[a]anthracene

Abstract

The DNA binding of nonreactive model compounds of metabolites of 7,12-dimethylbenz[a]-anthracene (DMBA)¹ was studied in fluorescence quenching and fluorescence lifetime experiments. The model compounds examined were DMA and 8,9,10,11-tetrahydro-BA. DMA is a π electron model of a highly carcinogenic bay region epoxide of DMBA. 8,9,10,11- tetrahydro-BA is a model compound of a less carcinogenic DMBA epoxide.

The results indicate that the binding of DMA occurs primarily via intercalation. In 15% methanol the binding constant is 3.1 × 10³M^?1. In 15% methanol and at DNA phosphate levels of 5.0 × ^?4 M the intercalative binding of DMA is reduced by a factor of 6.2 when 5.0 × 10^?4 M Mg⁺² is added. The DMA binding constant for intercalation is reduced by more than a factor of 4 when the methanol content of the solvent is increased from 0% to 20%. Finally DMA binding arising from π interactions with the DNA bases is reduced more than 15 times when the DNA is denatured. For 8,9,10,11-tetrahydro-BA in 15% methanol the binding constant for intercalation is 6 times lower than that for DMA.

These results along with previously reported binding data on other model compounds suggest that bay region metabolites of DMBA readily participate in physical π stacking interactions with DNA.     

Fluorescence of free and protein-bound Auramine O

The spectral properties and binding of Auramine O were studied as a model for the binding of cationic ligands to proteins. The dye was fluorescent in H₂O with a quantum yield of 4 × 10^?5, but the emission became blue-shifted and more intense in less polar solvents, as in the case of more common fluorescent probes. Emission increased where dye motion was restricted, e.g., when bound to proteins, in glycerol solutions, dried on filter paper, or embedded in ice. The amount of solvent spectral shift was probably limited by the short lifetime of free dye emission, which was estimated to be of the order of picoseconds. Auramine O was bound by yeast alcohol dehydrogenase and serum albumins of different species. Fluorescence enhancement and equilibrium dialysis measurements showed the number of dyes bound per molecule of protein and the association constants to be 2 and 1.2 × 10⁴m^?1 for yeast alcohol dehydrogenase and 1 and 0.23–1.9 × 10⁴m^?1 for the albumins. The Auramine O complex with liver alcohol dehydrogenase, described by Conrad et al. [Biochemistry9, 1540–1546 (1970)], had peak emission at 520 nm, further to the red than any of the other complexes studied, suggesting a relatively polarizable binding environment. NaCl did not displace the dye, but enhanced its fluorescence in the complex. The fluorescence was sensitive to protein conformational changes brought about by urea. A literature survey suggests that cationic organic ligands bind strongly to the active site of only those enzymes which have cationic substrates, and bind only weakly to noncatalytic sites in other enzymes. The significance and advantages of cationic fluorescent probes of proteins are discussed.     

Spectral manifestations of different types of acriflavine binding to DNA in ultraviolet and visible region]

Difference absorption spectra (complex-sum of the initial reagents) are obtained in the visible and longwave UV region for the system of actiflavine and DNA in a number of cases differing in initial and final degrees of DNA filling by the dye, in particular separately for two types of dye binding to DNA. For these binding types conventional absorption spectra are calculated. In the visible region for the first binding type ("strong" binding) red shift of the absorption band is observed; for the second type ("weak" binding) we observed splitting of the band, short wavelength component being highly prevailing, and hypochromism. In the UV region for both binding types the spectra changed in approximately similar way; a slight blue shift and a rather remarkable hypochromism are observed. It is shown that the dye brings the main contribution into the spectral changes in the UV region. If to take into account the spectral properties of molecular aggregates the data obtained are compatible with the intercalation model for "strong" binding and dye stacking on DNA for "weak" binding.     

Evaluation of the effect of Tb(IV)-NR complex on herring sperm DNA genetic information by mean of spectroscopic

Abstract

The interaction between Tb(IV)-NR complex and herring sperm DNA in buffer solution of Tris-HCl was investigated with the use of acridine orange(AO) as a spectral probe. The binding modes and other information were provided by the UV–spectrophotometry and fluorescence spectroscopy. The thermodynamic functions expressed that the binding constants of Tb(IV)-NR complex with DNA was K^θ_298.15K = 4.03?×?10⁵?L·mol^?1, K^θ_310.15K =1.30?×?10⁷?L·mol^?1, and the Δ_rGθ m _298.15?K＝?3.20?×?10⁴ J·mol^?1. The scatchard equation suggested that the interaction mode between Tb(IV)-NR complex and herring sperm DNA is electrostatic and weak intercalation bindings. FTIR spectroscopy results also indicate that there is a specific interaction between the Tb(IV)-NR complex and the A and G bases of DNA.     

Stereospecific 3H-nicotine binding to intact and solubilized rat brain membranes and evidence for its noncholinergic nature

³H-nicotine binding was performed on intact and solubilized rat brain membranes as well as membranes from the electric organ of the $\text{Torpedo}$ fish. The K_d for binding to intact and solubilized rat brain membranes was 5.6 × 10^?9 M and 1.1 × 10^?8M respectively, and the binding capacity 2.0 × 10^?14 and 3.0 × 10^?13 moles /mg protein respectively. The K_d for Torpedo membranes was 3.1 × 10^?7M and the binding capacity 6.8 × 10^?13 moles/mg protein. The binding was stereospecific with the affinity of the (?)-nicotine being about 8 times greater than the (+)-nicotine with all three preparations. The relative affinity for the nicotine binding site of nicotinic cholinergic drugs was considerably less in rat brain than in $\text{Torpedo}$ membranes, where the sites are mainly cholinergic. A comparison was made of the ability of a variety of cholinergic drugs and nicotine derivatives to compete with ³H-nicotine binding and their relative pharmacologic potency to produce or inhibit a characteristic prostration syndrome caused by (?)-nicotine administered intraventricularly to rats. From such studies it was concluded that nicotine, in part, may be interacting at noncholinergic sites in rat brain.     

Muscarinic cholinergic binding sites in the developing avian heart.

The potent muscarinic cholinergic antagonist 3-quinuclidinyl benzylate (QNB) has been used to detect and quantify muscarinic receptors in the developing chick heart. Specific binding in microsomal pellets prepared from hearts ranging in age from 70 hr in ovo to adulthood was examined and was found to increase from 4 × 10^?13 moles of [³H]QNB bound/mg of protein at the earliest stage tested to 5 × 10^?12 moles of [³H]QNB/mg of protein at birth and then to drop slightly to 2 × 10^?12 moles of [³H]QNB/mg of protein at the latest age tested. The developmental significance of these results is discussed.     

Characterization of a hormone receptor defect in the androgen-insensitivity mutant

Mouse kidney cytosol contains specific receptors that reversibly bind dihydrotestosterone at a concentration of 43 f moles/mg protein. [Nonstandard abbreviation: DHT, dihydrotestosterone, 17 β-hydroxy-5 α-androstan-3-one.] The equilibrium dissociation constant of the receptor-dihydrotestosterone complex is 1.3 × 10^?9M for females and 1.7 × 10^?9M for castrated males. The complex sediments at 8–9S in glycerol gradients. In males bearing the androgen-insensitivity mutation (analogous to human testicular feminization), the specific dihydrotestosterone receptor activity is decreased about 8 fold. The residual binding activity has wild type affinity (K_D = 1.5 × 10^?9M) for dihydrotestosterone and also sediments at 8–9S. Kidney cytosol from castrated mutant mice displays a new binding component with low affinity and high capacity for dihydrotestosterone.     

Kinetics of the stacking of ethidium bromide by the raman laser temperature-jump method

Raman laser temperature-jump measurements have been made on concentrated solutions of ethidium bromide. Two relaxations were observed. The faster has a lifetime of less than 30 ns and is attributed to rotation of the phenyl ring. The slower relaxation is concentration dependent and is due to the parallel stacking of two dye molecules. The forward and reverse rates for this process are (4.6 ± 1.4) × 10⁸ M^?1s^?1 and (6.7 ± 1.4)× 10⁶ s^?1, respectively, at 25°C. 0.25 M ionic strength, and pH 6.9. This reverse rate and those of three similar reactions are found to fit a linear free energy plot. The implications of these results for studies of nucleic acid base stacking are discussed.     

Intercalation of manganese-mefenamic acid complex into double stranded of calf thymus DNA

Abstract

The interaction of the [Mn(mef)₂(phen)H₂O] complex in which mef is mefenamic acid drug and phen is 1,10 phenanthrolin ligand with calf thymus DNA (ct-DNA) was studied by using different spectroscopic methods, molecular docking and viscometery. The competitive fluorescence and UV–Vis absorption spectroscopy indicated that the complex interacted with ctDNA via intercalating binding mode with the binding constant of 1.16?×?10⁴ Lmol^?1. The thermodynamic studies showed that the reaction between the complex and ctDNA is exothermic. Furthermore, the complex induced changes in DNA viscosity. Circular dichroism spectroscopy (CD) was employed to measure the conformational changes of ctDNA in the presence of the complex and verified intercalation binding mode. The molecular modeling results illustrated that the complex interacted via intercalation by relative binding energy of ?28.45?kJ mol^?1.     

Synthesis,Characterization, Molecular Modeling,and DNA Interaction Studies of Copper Complex Containing Food Additive Carmoisine Dye

A copper complex of carmoisine dye; [Cu(carmoisine)₂(H₂O)₂]; was synthesized and characterized by using physico-chemical and spectroscopic methods. The binding of this complex with calf thymus (ct) DNA was investigated by circular dichroism, absorption studies, emission spectroscopy, and viscosity measurements. UV-vis results confirmed that the Cu complex interacted with DNA to form a ground-state complex and the observed binding constant (2× 10⁴ M^?1) is more in keeping with the groove bindings with DNA. Furthermore, the viscosity measurement result showed that the addition of complex causes no significant change on DNA viscosity and it indicated that the intercalation mode is ruled out. The thermodynamic parameters are calculated by van't Hoff equation, which demonstrated that hydrogen bonds and van der Waals interactions played major roles in the reaction. The results of circular dichroism (CD) suggested that the complex can change the conformation of DNA from B-like form toward A-like conformation. The cytotoxicity studies of the carmoisine dye and its copper complex indicated that both of them had anticancer effects on HT-29 (colon cancer) cell line and they may be new candidates for treatment of the colon cancer.     

Thermodynamics of mucopolysaccharide–dye binding. II. Binding constant and cooperativity parameters of acridine orange–dermatan sulfate system

In the acridine orange–dermatan sulfate system, free and bound dye can be distinguished from each other spectroscopically. This permits the use of fluorometric methods to study the binding of acridine orange to the acid mucopolysaccharide dermatan sulfate. Experiments were conducted at 24°C in 10^?3 M citrate/phosphate buffer at pH = 7.0. The binding of the dye is highly cooperative, as evidenced by considerable interaction between adjacent bound dye molecules. Analysis of the data indicates that dermatan sulfate binds 2.3 ± 0.3 mol of acridine orange per dermatan sulfate uronic acid residue with a cooperative binding constant, K_q ranging from 4.9 to 6.0 × 10⁵ M^?1 which corresponds to a free energy of 7.74 ? ΔG° ? 7.86. The cooperativity parameter q apparently increases with increasing polymer-to-dye ratio.     

Salt bridge exchange binding mechanism between streptavidin and its DNA aptamer – thermodynamics and spectroscopic evidences

Protein‐nucleic acids binding driven by electrostatic interactions typically are characterized by the release of counter ions, and the salt‐inhibited binding association constant (K_a) and the magnitude of exothermic binding enthalpy (ΔH). Here, we report a non‐classical thermodynamics of streptavidin (SA)–aptamer binding in NaCl (140–350 mM) solutions near room temperatures (23–27 °C). By using isothermal titration calorimetry (ITC) and circular dichroism (CD)/fluorescence spectroscopy, we found that the binding was enthalpy driven with a large entropy cost (ΔH ?20.58 kcal mol^?1, TΔS ?10.99 kcal mol^?1, and K_a 1.08 × 10⁷ M^?1 at 140 mM NaCl 25 °C). With the raise of salt concentrations, the ΔH became more exothermic, yet the K_a was almost unchanged (ΔH ?26.29 kcal mol^?1 and K_a 1.50 × 10⁷ M^?1 at 350 mM NaCl 25 °C). The data suggest that no counter Na⁺ was released in the binding. Spectroscopy data suggest that the binding, with a stoichiometry of 2, was accompanied with substantial conformational changes on SA, and the changes were insensitive to the variation of salt concentrations. To account for the non‐classical results, we propose a salt bridge exchange model. The intramolecular binding‐site salt bridge(s) of the free SA and the charged phosphate group of aptamers re‐organize to form the binding complex by forming a new intermolecular salt bridge(s). The salt bridge exchange binding process requires minimum amount of counter ions releasing but dehydration of the contacting surface of SA and the aptamer. The energy required for dehydration is reduced in the case of binding solution with higher salt concentration and account for the higher binding exothermic mainly. Copyright © 2013 John Wiley & Sons, Ltd.     

A New Heteroleptic Ruthenium Sensitizer for Transparent Dye‐Sensitized Solar Cells

A new heteroleptic ruthenium complex, coded CYC‐B19 , incorporating an ancillary ligand endowed with hexylthio‐bithiophene segments and a conjugated anchoring ligand with vinyl groups was prepared. This new sensitizer exhibits a lower energy MLCT band centred at 562 nm with a remarkably high molar absorption coefficient of 2.97 × 10⁴ M^?1 cm^?1. DFT‐TDDFT theoretical calculation revealed that insertion a vinyl group in the anchoring ligand pushes the LUMO electron locating more on the anchoring ligand. This will benefit the electron transfer from dye to TiO₂ when the dye molecules were excited by light. Physicochemical measurements and the optimization of electrolyte were done to investigate the potential of CYC‐B19 in TiO₂ scattering‐layer free dye‐sensitized solar cells. Not only is a good photovoltaic efficiency of 8.4% reached, but the transparent device sensitized by CYC‐B19 also presents a superior spectral response to its predecessor CYC‐B11 .     

DNA binding of a proflavine derivative bearing a platinum hanging residue

New platinum(II) complex of 3,6-diamine-9-[6,6-bis(2-aminohethyl)-1,6-diaminohexyl]acridine, AzaPt, has been synthesised and characterised. Behaviour of AzaPt in solution (protonation and possible self-aggregation phenomena) has been investigated by spectral methods (absorbance and fluorescence) at I = 0.1 M and 25 °C, and the equilibrium parameters of binding to calf thymus DNA have been established. Two different modes of DNA binding by the complex were detected, which depend on the polymer to dye molar ratio (P/D). At relatively low P/D values the mode was interpreted as binding by the polyamine residue external to the base pairs, while at high P/D values the binding corresponds to intercalation of the proflavine residue. Such interpretation is supported by the observed salt effect on binding and the temperature variation of the binding constants, which allowed estimating the ΔH and ΔS values contributions. Spectrophotometric analysis of the long time range binding revealed that AzaPt is involved in a slow reaction, interpreted as an attack by the platinum ion on the nucleobases. The time constant for such interaction was calculated and found to be the same order of magnitude as for processes responsible for the action of anti-tumour drugs that do covalently bind to polynucleotides.     

Interacalation of ethidium ion into DNA and RNA oligonucleotides

The thermodynamics of ethidium ion binding to the double strands formed by the ribooligonucleotides rCA₅G + rCU₅G and the analogous deoxyribo-oligonucleotides dCA₅G + dCT₅G were determined by monitoring the absorbance versus temperature at 260 and 283 nm at several concentrations of oligonucleotides and ethidium bromide. A maximum of three ethidium ions bind to the oligonucleotides, which is consistent with intercalation and nearest-neighbor exclusion. For the ribo-oligonucleotide the binding mechanism is complex. Either two sites (assumed to be the intercalation sites at the two ends of the oligonucleotide) bind more strongly by a factor of 140 than the third site, or all sites are identical, but there is strong anticooperativity on binding (cooperativity parameter, 0.1). In sharp contrast, the binding to the same sequence (with thymine substituted for uracil) in the deoxyribo-oligonucleotide showed all sites equivalent and no cooperativity. For the ribo-oligonucleotides the enthalpy for ethidium binding is ?14 kcal/mol. The equilibrium constants at 25°C depend on the model; either K = 6 × 10⁵M^?1 for the two strong sites (4 × 10³M^?1 for the weak site) or K = 2.5 × 10⁵M^?1 for the intrinsic constant of the anticooperative model. For the equivalent deoxyribo-oligonucleotide the enthalpy of binding is -9 kcal/mol and the equilibrium constant at 25°C is a factor of 10 smaller (K = 2.5 × 10⁴M^?1).     

S-adenosylmethionine pool size and turnover rate in sea urchin embryos determined from simultaneous measurements of amounts and specific activities.

A procedure is presented for the simultaneous measurement of the tissue pool size and specific activity of methyl-labeled S-adenosylmethionine (SAM). The method of Kopin and Baldessarini (1971) is used with the introduction of a reference amount of SAM, methyl-labeled with a second isotope to provide an isotope dilution by the tissue sample. The SAM pool sizes in two species of sea urchin embryo were approximately constant during development from blastula to gastrula, being 6.8 and 6.3 × 10^?14 moles/embryo at these respective stages for Strongylocentrotus purpuratus and 15.7 and 14.2 × 10^?14 moles/embryo for Lytechinus pictus. The rates of turnover of SAM in the gastrulae of these two species are at least 2.7 × 10^?15 and 5.2 × 10^?15 moles/min/embryo, respectively.     

Rapid kinetic studies of calmodulin interactions with calcium and troponin I as monitored by anthroylcholine fluorescence

Anthroylcholine was utilized as an extrinsic fluorescent probe in rapid kinetic studies of calcium dissociation from calmodulin (k_off = 10 S^?1) and the calmodulin-troponin I complex (k_off = 6 S^?1). At concentrations lower than 70 μM, the mechanism of dye binding agreed with the simple kinetic scheme in which the dye binds exclusively to the respective calcium complexes of calmodulin and calmodulin-troponin I. The sensitivity of anthroylcholine also made possible the estimation of values for the association (1.0 ± 0.8) × 10⁸$\text{M}{}^{\mathrm{?1}}$ S^?1) and dissociation rate constants (2 ± 170 S^?1) for troponin I binding to the calcium₄-calmodulin complex.