Studies on sildenafil citrate (Viagra) interaction with DNA using electrochemical DNA biosensor

The interaction of sildenafil citrate (Viagra) with DNA was studied by using an electrochemical DNA biosensor. The binding mechanism of sildenafil citrate was elucidated by using constant current potentiometry and differential pulse voltammetry at DNA-modified glassy carbon electrode. The decrease in the guanine oxidation peak area or peak current was used as an indicator for the interaction in 0.2M acetate buffer (pH 5). The binding constant (K) values obtained were 2.01+/-0.05 x 10(5) and 1.97+/-0.01 x 10(5)M(-1) with constant current potentiometry and differential pulse voltammetry, respectively. A linear dependence of the guanine peak area or peak current was observed within the range of 1-40 microM sildenafil citrate with slope=-2.74 x 10(-4)s/microM, r=0.989 and slope=-2.78 x 10(-3)microA/microM, r=0.995 by using constant current potentiometry and differential pulse voltammetry, respectively. Additionally, binding constant values for sildenafil citrate-DNA interaction were determined for the pH range of 4-8 and in biological fluids (serum and urine) at pH 5. The influence of sodium and calcium ions was also studied to elucidate the mechanism of sildenafil citrate-DNA interaction under different solution conditions. The present study may prove to be helpful in extending our understanding of the anticancer activity of sildenafil citrate from cellular to DNA level.     

Studies on the interaction between polyion and counterions by sound velocity (II)

Sound velocities in polyacrylate solutions neutralized by tetraalkylammonium hydroxide were measured at various concentrations of added NACl. From the results, the degree of counterion binding to polyion and the extent of the changes in hydration volume due to ion binding were determined as a function of the degree of neutralization, alpha. The ion binding accompanying the volume changes appeared above about alpha = 0.6 and the ion binding process depended on the charge density of the polyion. The effect of the size of the tetraalkylammonium ion on ion binding was negligibly small.     

On the mechanism of interaction between histone II B1 and DNA and histone II B2 and DNA

A mechanism is suggested at the molecular level whereby histone IIB₂ can act as a cross-link between two (or possibly three) adjacent and parallel strands of DNA double helix some 40 Å apart. Application of Prothero's rule and the Lewis probability functions indicate the probable locations of three a-helices and a number of β-turns. This, coupled with the requirement that the tertiary conformation of the histone be complementary to the DNA molecules and for as many basic groups as possible to bind to phosphate oxygens, allows us to suggest, on the basis of model building using accurate space-filling (CPK) models, a complex conformation that achieves this.A similar process applied to histone IIB₁, whose complete amino acid sequence is also known, shows the location of five probable a-helices, a number of β-turns, and a segment of β-pleated sheet. The basic amino acids are gathered in four groupings. Model building experiments suggest that histone IIB₁ forms a complex strut joining four parallel strands of DNA double helix that form a diamond with diameters 100 and 40 Å. In both these models the purpose and function of a fair proportion of the individual amino acids can be specified.This paper is the third and last of a series in this Journal in which models are presented for the tertiary conformation and function of all five histones of known (in whole or in part) amino acid sequence. This suggests that all five are concerned in packing the long DNA double helix, which may be in a “square helix” form, into the confined space of the chromosome. The hypotheses may be tested by a direct investigation of nucleoprotein in situ to see if these 40, 70, and 100 Å interhelical distances can be detected by biophysical methods.     

Studies on the interaction between Cd(2+) ions and DNA

Cadmium is a potent carcinogen in rodents and has recently been accepted by the International Agency for Research on Cancer as a category 1 (human) carcinogen, but the molecular mechanism of its action remains largely unclear. It has however been suggested that cadmium-induced carcinogenesis may involve either direct or indirect interaction of Cd²⁺ with DNA. Cd²⁺ is believed to bind covalently with N7 centres of adenine and guanine. At low concentrations (≤50 mM), Cd²⁺ is found to react with plasmid DNA to produce a mixture of Form I and Form II bands whereas at higher concentrations (≥100 mM), Cd²⁺ causes extensive damage to DNA at a pH 5.8 solution of cadmium nitrate. Within the range 0–100 mM (when pH is adjusted to 7.4 by adding NaOH) an increase in concentration of Cd²⁺ is found to cause a decrease in the gel mobility rate of plasmid and an increase in the intensity of the Form II band. When plasmid DNA is digested with BamH1, only the Form III band is observed both in the presence and absence of Cd²⁺. However, the mobility of the band is found to decrease with the increase in the concentration of Cd²⁺. When the enzyme Ssp1 which cuts plasmid DNA at the AT sites is used instead of BamH1, two bands are observed in the presence of cadmium as against one band in the absence of cadmium. These results suggest that Cd²⁺ binds covalently with DNA (possibly at G, A and T centres) and can form intrastrand bifunctional AT adducts but not the GG adducts. It may also be that neither GG nor AT adducts are formed and yet Ssp1 digestion is prevented because of a structural modification introduced in adenine by its interaction with Cd²⁺. In the presence of antioxidants such as cysteine, glutathione and ascorbate (especially cysteine and ascorbate), DNA damage is found to be greater than expected for the combined effects of the antioxidant and Cd²⁺. The increased DNA damage is believed to be due to the formation of reactive oxygen species (ROS).     

A spectroscopic and electrochemical study of the interaction between copper (II) glycylglycyl-L-histidine-N-methylamide and iron (III) tetra-p-sulfophenylporphine

A binuclear complex has been produced by the reaction of an iron porphyrin (sodium tetra-p-sulfophenylporphine iron (III)-FeTPPS) with a copper metallo-tripeptide (copper (II) glycylglycyl-L-histidine-N-methylamide-CuGGH) in aqueous solution. The system has been characterized by electron spin resonance (ESR) spectroscopy, optical absorption spectroscopy, and electrochemical methods. Room-temperature ESR spectra of the copper complex and low-temperature ESR spectra of the iron porphine provide evidence for the formation of a binuclear complex. These findings are supported by absorption spectroscopy and electrochemical studies, and lead to a value of ca. 2 X 10(-3) M-1 (at room temperature) for the equilibrium constant for complex formation. The relevance of this system to the enzymic active site of mammalian cytochrome c oxidase is discussed.     

Studies on the interaction between Ag(+) and DNA

The interaction between silver ion and DNA has been followed by submarine gel electrophoresis. When pBR322 plasmid DNA was allowed to interact with silver(I) acetate, it was found to contain Form I and Form II bands whose intensity remained unchanged as the concentration of Ag(+) was increased from 0 to 50 mM. However, the mobility of the bands decreased as the concentration of Ag(+) was increased, indicating the occurrence of increased covalent binding of the metal ion with DNA. When 1:1 mixtures of silver(I) acetate and ascorbate were allowed to interact with plasmid and genomic DNAs, it was found that the mixtures were much more damaging to plasmid as well as genomic DNAs than silver(I) acetate or ascorbate alone. In the case of pBR322 plasmid DNA, the mixture at 12.5 mM concentration was found to be more damaging than the mixtures at both higher and lower concentrations. The increased DNA damage is believed to be due to free radicals produced from the oxidation of ascorbate by molecular oxygen where the metal ion was playing a catalytic role.     

Studies on the interaction between steffimycins and DNA.

The complexes formed between steffimycins and DNA were studied using various physicochemical techniques. The binding process has been followed spectrophotometrically or fluorimetrically. The binding parameters n and K, evaluated according to McGhee and Von Hippel, show a good affinity of these antibiotics for the macromolecule. Flow dichroism measurements showed that in the complex with DNA, the antracycline moiety of the steffimycins is intercalated between two base pairs of the macromolecule. The binding experiments with various polydeoxyribonucleotides and with various DNA samples, having different base pair compositions, suggest that an alternate sequence of A-T, such as that of poly[d(A-T)] . poly[d(A-T)], represents a good receptor site for the binding of steffimycins to DNA. The lack of in vivo activity of these antibiotics is discussed.     

Studies on the interaction of altromycin B and its platinum(II) and palladium(II) metal complexes with calf thymus DNA and nucleotides

The interaction of the anticancer antibiotic altromycin B and its isostructrural Pt(II) and Pd(II) metal complexes with native calf thymus (CT) DNA was studied using UV-thermal denaturation experiments, circular dichroism spectroscopy and temperature controlled spectrophotometric titrations. Altromycin B stabilizes the double helix by raising the T(m), mainly by intercalation of its chromophore between the base pairs and interacting electrostatically via its sugar moieties with the edges of the DNA helix. Moreover, altromycin B induces a B-->A structural transition of CT DNA. The effect on DNA stability and conformation depends on the metal ion. Pt(II) and Pd(II) complexes induce the B-->A structural transition and stabilize the double helix similarly but they present lower final hyperchromicity due to premelting effects which were caused by intra- and interstrand crosslinking. Thus, a synergic effect of the metal ions to altromycin B-CT DNA interaction is observed in both cases. Altromycin B interacts with 5'-GMP, 5'-AMP and 5'-CMP by electrophilic attack of the opened epoxide ring to the N(7)G, N(1)/N(7)A and N(3)C. Thus, covalent binding between these nucleotides and altromycin B takes place and explain the multiple binding mode suggested by the studies of the interaction of altromycin B and its complexes with DNA. The [Pd(II)-altroB] complex dissociates in the presence of the nucleotides, and various species of Pd(II)-nucleotide complexes, especially with 5'-GMP, are formed. The [Pt(II)-altroB] complex dissociates too, but only one or two species of Pt(II)-nucleotide complexes are formed, and in the case of 5'-AMP interaction the formation of a tertiary altroB-Pt(II)-5'AMP complex is proposed. 5'-TMP reacts very weakly in comparison with the other three nucleotides. These interactions were followed by 1H-NMR.     

Studies on the mechanism of interaction between rabbit transferrin and reticulocytes

The two stages in the uptake of transferrin by rabbit reticulo-cytes were investigated using radioiodine-labeled rabbit transferrin and albumin. The first stage of rapid, temperature-insensitive uptake of transferrin was similar to albumin uptake: uptake of both proteins increased linearly with increasing protein concentration of the incubation medium up to at least 60 mg/ml, was maximal at low ionic strength and pH, and increased in the presence of basic polyamino acids. Transferrin uptake was in part dependent on the reticulocyte concentration of the blood, but albumin uptake was independent of reticulocyte concentration. The second slower, temperature-sensitive stage of transferrin uptake was linearly related to reticulocyte concentration, and was not found with albumin, α¹-macroglobulin or γ-globulin. Transferrin uptake was optimal at physiological pH and ionic strength and was unaffected by basic polyamino acids. When the transferrin concentration was raised, uptake increased to reach a maximum at a concentration of 15 mg/ml. It was concluded that the first stage of transferrin uptake was in part or wholly due to non-specific adsorption of transferrin to erythrocytes, while the second stage of uptake was specific for transferrin and reticulocytes and depended upon normal function of the cells.     

Studies on interaction between poly(L-lysine) and DNA of varied G + C contents

Interaction between polylysine and DNA's of varied G + C contents was studied using thermal denaturation and circular dichroism (CD). For each complex there is one melting band at a lower temperature t_m, corresponding to the helix–coil transition of free base pairs, and another band at a higher temperature t′_m, corresponding to the transition of polylysine-bound base pairs. For free base pairs, with natural DNA's and poly(dA-dT) a linear relation is observed between the t_m and the G + C content of the particular DNA used. This is not true with poly(dG)·poly(dC), which has a t_m about 20°C lower than the extrapolated value for DNA of 100% G + C. For polylysine-bound base pairs, a linear relation is also observed between the t′_m and the G + C content of natural DNA's but neither poly(dA-dT) nor poly(dG)·poly(dC) complexes follow this relationship. The dependence of melting temperature on composition, expressed as dt_m/dX_G·C, where X_G·C is the fraction of G·C pairs, is 60°C for free base pairs and only 21°C for polylysine-bound base pairs. This reduction in compositional dependence of T_m is similar to that observed for pure DNA in high ionic strength. Although the t′_m of polylysine-poly(dA-dT) is 9°C lower than the extrapolated value for 0% G + C in EDTA buffer, it is independent of ionic strength in the medium and is equal to the t_m⁰ extrapolated from the linear plot of t_m against log Na⁺. There is also a noticeable similarity in the CD spectra of polylysine· and polyarginine·DNA complexes, except for complexes with poly(dA-dT). The calculated CD spectrum of polylysine-bound poly(dA-dT) is substantially different from that of polyarginine-bound poly(dA-dT).     

Hydrogen-bonded supramolecular manganese(II) complexes with network and sheet structures bridged by terephthalate unit

Two 1D complexes [Mn(4- methylpyrazole)₃(H₂O)(tp)]_n (2) and [Mn(4-methylpyrazole)₄(tp)]_n (3) (tp = terephthalate) were synthesized and characterized by means of X-ray analysis and magnetic studies. The molecular structure of 2 reveals that Mn(II) centers with asymmetric coordination surroundings are bridged by crystallographically different tp ligands, forming a 1D chain. The 1D coordination chains are interconnected by hydrogen bonds between free carboxylate oxygen atoms in a chain and hydrogens of pyrazole nitrogen atoms in neighboring chains, leading to a 3D framework. Compound 3 also exhibits a 1D coordination chain which is hydrogen-bonded to adjacent chains, providing a 2D sheet structure. Interestingly, the structures include intra- and interchain hydrogen bonds contributed from N-H groups of the capping 4-methylpyrazole ligands. Magnetic measurements show weak antiferromagnetic interactions with exchange coupling parameters of J = −0.018 cm⁻¹ for 2 and J = −0.062 cm⁻¹ for 3 through the extended tp ligand on the basis of an infinite chain model (H = −J∑S_i · S_i + 1).     

Electrochemical and spectroscopic evidences of the interaction between DNA and Pt(II)(dppf)-complex

The interaction of Pt(II)(dppf)-complex, namely [Pt(dppf)(H₂O)₂]²⁺ with DNA was investigated by DPV and ¹H-NMR techniques. The results showed that the interaction process has been characterized by changes in the electrochemical parameters of both compounds and the formation of a new anodic current peak close to the anodic current peak of the [Pt(dppf)(H₂O)₂]²⁺. In addition, the ¹H-NMR spectra show that the coordination of Pt(II)(dppf)-complex to dsDNA occurs via N(7) of guanine. Others parameters like pH and ionic strength that affect the interaction process were also investigated.     

Studies on the interaction between antitrypanosome cis-DDP analogs with DNA

The nature of the conformational changes produced in DNA by cis-DDP analogs has been studied by physiochemical techniques. The UV spectra showed that the DNA undergoes bathochromic shifts accompanied by hyperchromic effects in reaction with specific analogs (cis-Pt(DDH) (mucobromic)2, cis-Pt(tranilcypromine)2Cl2 and cis-Pt(DDH) Cl2), while a different series of analogs (cis-Pt(DDH) (metafluorobenzoic)2 and cis-Pt(pentamidine)Cl2) induce a significative decrease in the absorbance at 258 nm. Moreover one of these analogs (cis-Pt(pentamidine)Cl2) causes strong stabilization of the double helix to heat denaturation. The CD spectra indicate moreover that cis-Pt(pentamidine)Cl2 modifies the secondary structure of the DNA in a significant way with an increase of the positive band and a decrease of the ellipticity of the negative band. The antitrypanosome activity of cis-Pt(pentamidine)Cl2 is probably due to inhibition of the intracellular parasites division in parasitized cells.     

Studies of interaction between poly(allylamine hydrochloride) and double helix DNA by spectral methods

DNA interaction with cationic polyelectrolytes promises to be a versatile and effective synthetic transfection agent. This paper presents the study on interaction between a simple artificial cationic polymer, poly(allylamine hydrochloride) (PAA), and herring sperm DNA (hsDNA) using several spectroscopic methods, including light scattering, microscopic FTIR-, CD-spectroscopy and so on. The results show that PAA interacts with DNA through both the phosphate groups and the nitrogenous bases of DNA. The formation of DNA/PAA complex may change the micro-environment of double helix of DNA from B- to C-form and the great changes in DNA morphology occur when N:P ratio is near to 1.0. At the same time, the spectroscopic changes of ethidium bromide (EB) on its binding to DNA are utilized to study the interaction between PAA and DNA. Reversion of the maximum absorption wavelength (numax), reduction of induced circular dichroism and decrease in fluorescence intensity of DNA-EB on addition of PAA indicate that the formation of the complex between DNA and PAA is not in favor of the interaction between DNA and EB. The binding constant of EB and the number of binding sites per nucleotide decrease with increase in the concentrations of PAA, indicating noncompetitive inhibition of EB binding to DNA in the presence of PAA. It is also proved that the formation of the DNA/PAA complex is influenced by pH value and ionic strength.     

The interaction of Rh(II) and Rh(III) with DNA

The interaction of Rh2(II)(acetate)4, cis-[Rh(III)(en)2Cl2] Cl (en = ethylenediamine) and [Rh(III) (NH3)5Cl]Cl2 with calf thymus DNA has been studied at various r values [formula; see text] and interaction times. Electronic spectra, melting and cooling curves and sedimentation data indicate no interaction of the acetate complex with DNA, except in the case of a high r value and long interaction time. The other two complexes have been found to interact with the phosphate groups, thus stabilizing the macromolecule.     

鹅膏毒肽与RNA聚合酶II相互作用的分子机制研究

研究鹅膏毒肽与RNA聚合酶II相互作用的分子机制,利用分子对接方法获得了9种鹅膏毒肽与RNA聚合酶II相互作用的结合模式、结合位点、对接能和抑制常数等信息,并对鹅膏毒肽的毒性与结构间的构效关系进行了考察。结果表明：利用分子对接方法获得的鹅膏毒肽与RNA聚合酶II相互作用的信息与实验结果相一致;不同R2取代基引起毒素与聚合酶II结合能力强弱不同,从而导致鹅膏毒肽分子间的毒性差异。结果证实了运用分子对接方法探索多肽分子与蛋白质相互作用的可行性,为在分子水平上研究多肽与蛋白质的相互作用开拓了新的思路。     

DNA interaction studies of tridentate bridged Ru(II)-Pt(II) mixed-metal supramolecules

Reported herein are studies of the concentration and temperature dependent interactions with DNA of the stereochemically defined mixed-metal supramolecular complexes, [(tpy)Ru(tppz)PtCl](PF₆)₃ and [ClPt(tppz)Ru(tppz)PtCl](PF₆)₄ (tpy = 2,2′:6′,2′′-terpyridine and tppz = 2,3,5,6-tetrakis(2-pyridyl)pyrazine). These metal complexes couple a ruthenium based light absorber (LA) to the bioactive platinum sites (BAS) using a tridentate bridging ligand (BL). The complexes exhibit intense Ru → tppz(π∗) metal to ligand charge transfer (MLCT) transitions in the visible region and adopt a square planar geometry around the Pt(II) center. The effect of incubating these metal complexes with DNA on the subsequent migration of DNA through an agarose gel was found to be more dramatic than that observed for the well known anticancer drug, cis-[Pt(NH₃)₂Cl₂] (cisplatin). This effect was enhanced with increased incubation temperature. Unwinding of supercoiled plasmid DNA was found to be more pronounced for the trimetallic complex, [ClPt(tppz)Ru(tppz)PtCl](PF₆)₄, than for the bimetallic complex, [(tpy)Ru(tppz)PtCl](PF₆)₃.     

Effects of imidazole and zinc on the interaction of some amino acid compounds of copper(II) with hydrogen peroxide

A novel effect of the inhibition of the decomposition of amino acids to carbonates on addition of imidazole (HIm) to a reacting system containing equimolar amounts of copper and zinc metal powders, an amino acid [glycine (Hgly), aspartic acid (H₂Asp) or glycylglycine (H₂gg)] (1:1:2) and excess hydrogen peroxide (H₂O₂) resulting in formation of a mixed metal mixed ligand peroxo complex compound was observed, because in the absence of imidazole the corresponding reaction system yields only a mixed metal peroxo carbonate. For the resulting complex compounds, the homogeneity, i.e. [Cu(Zn)(O₂ ^2–)(Gly)₂(HIm)(H₂O)], [Cu(Zn)(O₂ ^2–)(Asp)(HIm)(H₂O)₂] or [Cu(Zn)₂(O₂ ^2–)₂(gg)(HIm)(H₂O)₄], molecular formula, presence of peroxo group and coordination environment were established by combined physicochemical evidence from elemental and thermogravimetric analysis in air and argon atmospheres, electron spin resonance and electronic and IR spectral data. It is noteworthy to mention that the corresponding carboxylic acids of the above-mentioned amino acids, i.e. acetic and succinic acids, either do not decompose to carbonates in the absence of imidazole or form novel homogeneous peroxo mixed metal mixed ligand complex compounds as described above in the presence of imidazole. This suggests an important and significant mutual influence (in vitro) of biologically active chromophores like peroxo ions, imidazole and amino groups in the above-mentioned chemical reactions containing bioactive metals such as copper and zinc.