Interaction of the mutagen ethidium bromide with DNA, using a carbon paste electrode and a hanging mercury drop electrode

The interaction of ethidium bromide (2,7-diamino-10-ethyl-9-phenylphenanthridinium bromide; EB) with double stranded (ds) calf thymus DNA and thermally denatured single stranded (ss) DNA was studied in solution and at the electrode surface by means of transfer voltammetry using a carbon paste electrode (CPE) as working electrode in 0.2 M acetate buffer, pH 5.0. As a result of intercalation of this dye between the base pairs of dsDNA, the characteristic peak of dsDNA, due to the oxidation of guanine residues, decreased and after a particular concentration of EB a new peak at +0.81 V appeared, probably due to the formation of a complex between dsDNA and EB. The non-intercalated EB gives another peak, but at an increased concentration of the dye. A similar behaviour was observed during the interaction of the dye with ssDNA.Furthermore, the interaction of EB with ds, ss and supercoiled (sc) DNA was studied at the hanging mercury drop electrode (HMDE) surface by means of alternating current voltammetry in 0.3 M NaCl and 50 mM sodium phosphate buffer (pH 8.5) as supporting electrolyte. dsDNA yields a smaller peak at −1.42 V (peak III) compared to the one yielded by ssDNA, since the latter is a relaxed and more accessible form. By addition of EB into the buffer solution an increase of peak III was observed in the dsDNA form as well as in ssDNA resulting from their interaction with EB. Furthermore, the appearance of peak III in covalently closed circular scDNA after exposure to increasing concentrations of EB is a result of the introduction of ‘free ends’ in DNA affecting its structural integrity.     

Aggregation and solution behavior of 5-(1-(4-carboxybutyl) pyridinum-4-yl) 10,15,20-tris (1-methylpyridinium-4-yl) porphyrin: A resonance light scattering, fluorescence and absorption spectroscopic study

Aggregation behavior of water soluble porphyrins, 5-(1-(4-carboxybutyl) pyridinum-4-yl) 10,15,20-tris (1-methylpyridinium-4-yl) porphyrin (5-CBPyP) in the presence of various concentrations of calf thymus DNA (ct-DNA) and sodium chloride were studied in comparison with meso-tetrakis (4-N-methyl pyridinum) porphyrin (TMPyP), by optical absorption, fluorescence and resonance light scattering (RLS) spectroscopies. Both porphyrins obey Beer’s law in extended range of concentration. Optical absorption and RLS measurements demonstrated nonaggregation for both porphyrins under increasing concentration of ct-DNA and NaCl. However, in comparison, 5-CBPyP had less tendency for aggregation that may be taken as an advantage for its probable application in photodynamic therapy of cancer. The trend of changes in absorption spectra of both porphyrins in the presence of ct-DNA indicates the homogeneous intercalation binding mode. The values of (2.81 ± 0.28) × 10⁶ M^?1 and (0.95 ± 0.09) × 10⁶ M^?1 were obtained for apparent binding constant of TMPyP and 5-CBPyP from analysis of optical absorption data, respectively. This indicates the less affinity of 5-CBPyP to ct-DNA in comparison with TMPyP. The binding of both porphyrins to ct-DNA quenches fluorescence emission of Ethidium bromide (EB) that is bound to ct-DNA. The quenching process obeys linear Stern-Volmer relationship indicating the displacement of EB from its binding sites by these porphyrins. The results of this technique also represent the intercalation mode of binding for both porphyrins and higher binding affinity of TMPyP compared with 5-CBPyP.     

两种荧光探针法研究三种非甾体抗炎药与DNA的相互作用

采用溴化乙锭(EB)和中性红(NR)两种荧光探针分别考察了三种非甾体抗炎药(吲哚美辛、舒林酸和托美丁)与DNA的相互作用, 采用荧光发射光谱和共振散射光谱技术得出了基本一致的结论: 吲哚美辛和舒林酸可以在一定程度上与DNA结合(舒林酸更强), 结合方式可能有嵌插作用, 也可能有药物分子在DNA双链表面的组装, 作用力来源于静电作用. 而托美丁几乎不与DNA作用, 因为其疏水性弱, 与DNA分子结合几率小.     

Electrochemical and Spectroscopic Studies on Interaction between Complex of Copper(Ⅱ) with Schiff Base Ligand and DNA

The crystal structure of ( [CuL (H2O) 2 ] (ClO4) 2 · 2H2O, CuL) (L ＝ N- (5-sulfosalicylidene)-4' -bromoaniline) was determined by means of X-ray crystallography. The interaction between CuL and salmon sperm DNA in a 0. 1 mol/L HOAc-NaOAc buffer solution (pH 5.10) was investigated by cyclic voltammetry and UV-Vis spectroscopy. A couple of redox peaks of CuL in the cyclic voltammograms(CV) can be seen at the glassy carbon electrode. It was found that the peak current of CuL decreased significantly with a negative shift of the peak potential in the presence of DNA compared with that in the absence of DNA. In addition,the decreased absorbance of CuL was observed with increasing the concentration of DNA; the absorption spectrum of an ethidium bromide(EB)-DNA system inthe presence of CuL confirms that the binding mode of CuL to DNA is different from the intercalation of EB with DNA. All the experimental results indicate that CuL can bind to DNA by electrostatic binding and form a 1:1 association complex with a binding constant of 2.72×104 L/mol.     

溴化乙锭对B-DNA碱基对特异性识别的分子模拟研究

溴化乙锭是一种常用的DNA荧光探针, 其作用机制是通过插入作用与DNA分子形成稳定的复合物. 分子模拟显示, 溴化乙锭插入碱基对过程中有大小沟选择性, 对结合能的统计分析发现, 溴化乙锭分子更倾向从小沟方向插入到DNA分子中. 由溴化乙锭从小沟方向插入不同碱基对的结合能考察发现, 溴化乙锭对DNA碱基对有特异性识别, 并且与CA碱基对结合能最强. 对溴化乙锭插入DNA分子的驱动力和序列特异性识别的作用力分析, 揭示溴化乙锭插入DNA分子的驱动力和碱基对的特异性识别均以静电作用为主.     

建筑用梳形共聚物分散剂溶液行为的光散射研究

采用激光光散射研究了一种主链为聚丙烯酸侧链为聚乙二醇的梳形共聚物分散剂的一些溶液行为.从静态光散射得出了较为合理的表观重均分子量、均方旋转半径等参数.动态光散射给出了流体力学半径分布及其角度和浓度依赖性.结合静态和动态光散射,上述梳形共聚物分散剂在溶液中的构象也得到初步的表征.通过与描述梳形聚合物的Gay-Raphae模型进行比较表明,这类梳形共聚物溶液在低盐离子和低pH值条件下存在聚集行为,形成以PAA主链为核PEG为壳层的类胶束聚集.     

The interaction of poly(ethylenimine) with nucleic acids and its use in determination of nucleic acids based on light scattering

For the first time, poly(ethylenimine) (PEI) was used to determine nucleic acids with a light scattering technique using a common spectrofluorometer. The interaction of PEI with DNA results in greatly enhanced intensity of light scattering at 300 nm, which is caused by the formation of the big particles between DNA and PEI. Based on this, a new quantitative method for nucleic acid determination in aqueous solutions has been developed. Under the optimum conditions, the enhanced intensity of light scattering is proportional to the concentration of nucleic acid in the range of 0.01-10.0 microg ml(-1) for herring sperm DNA (hsDNA), 0.02-10.0 microg ml(-1) for calf thymus DNA (ctDNA), 0.02-20.0 microg ml(-1) for yeast RNA (yRNA). The detection limits are 5.3, 9.9, and 13.7 ng ml(-1), respectively. Synthetic samples were determined satisfactorily. At the same time, the light scattering technique has been successfully used to obtain the information on the effects of pH and ionic strength on the formation and the stability of the DNA/PEI complex, which is important in some fields such as genetic engineering and gene transfer. Using ethidium bromide (EB) as a fluorescent probe, the binding of PEI with hsDNA was studied. Both the binding constant of EB with DNA and the number of binding sites per nucleotide decrease with increasing concentration of PEI, indicating noncompetitive inhibition of EB binding to DNA in the presence of PEI. And the association constant of PEI to DNA obtained is 1.2 x 10(5) M(-1). IR-spectra show that PEI interacts with DNA through both the phosphate groups and the bases of DNA and the formation of DNA/PEI complex may cause the change of the conformation of the DNA secondary structure, which is also proved by UV-spectra.     

水溶性桥联双卟啉与DNA相互作用的研究

以4,4'-二羧酸-2,2'-联吡啶为桥联试剂, 合成了一种含8个阳离子的水溶性桥联双卟啉(PD). 以5,10,15,20-四(4-N-甲基吡啶盐)卟啉(H₂TMPyP)为参照物, 使用紫外-可见光谱、荧光光谱、圆二色谱研究了水溶性双卟啉与小牛胸腺DNA (CT DNA)的相互作用, 以溴化乙啶(EB)竞争法测定了PD与CT DNA的表观键合常数(K_app)为1.2×10⁶ L•mol^－1 (H₂TMPyP为6.9×10⁶ L•mol^－1), 并使用凝胶电泳研究了PD对pBR322质粒DNA的切割能力. 实验结果表明PD与CT DNA的作用方式是插入和外部结合的混合模式.     

Surfactant encapsulated DNA: structure characterization and interaction with dye molecules in organic media

The recognition of electrostatically-bound DNA-didodecyldimethylammonium (DNA-DDDA) complex by three dye molecules, acridine orange (AO), ethidium bromide (EB) and 5,10,15,20-tetrakis(4-N-methylpyridyl) porphyrin tetra(p-toluenesulfonate) (TMPyP) in organic media was investigated through 1H NMR, UV-vis, and circular dichroism (CD) spectroscopies. When the organic solvent in which DNA-DDDA complex dissolves is changed from ethanol to chloroform, the adsorbed AO undergoes a reversible transformation from a monomer to a highly aggregated state at the interface between DNA and DDDA. EB also adsorbs at the interface between DNA and DDDA when EB interacts with the DNA-DDDA complex in organic media, but its existing state is independent of the used solvents. The third dye, TMPyP cation can intercalate into the G-C region while its anionic p-tosylate counterion remains unbound when it mixes with DNA complex in organic media. The complexes of DDDA with previously recognized DNA by the three dye molecules (DNA-dye), respectively, are also investigated. AO seems having changed its location from the grooves of DNA to the interface between DNA and DDDA after DNA-AO complex was electrostatically encapsulated with DDDA. The aggregation behavior of AO also shows a dependence on the polarity of the organic solvent. EB molecules are believed to intercalate into the base pairs of DNA in aqueous solution. The intercalation mode is still maintained after the encapsulation for DNA-EB in organic solvents, which is different from the situation between DNA-DDDA complex and EB. But in both cases, the existing states of EB are independent of the polarity of the organic solvents. Finally, TMPyP in the complex of DNA-TMPyP and DDDA is also judged to intercalate into the G-C region of DNA while its anionic p-tosylate counterion remains separated from DNA complex, which is similar to its interaction with DNA-DDDA complex in organic media. These data also strongly suggest that the intercalation state of TMPyP is more stable than its adsorption state in grooves when it is recognized with DNA. The present results are significant for the designs of both laser dye and conductive materials.     

Synthesis, cytotoxicity and spectroscopy studies of a new copper (II) complex: calf thymus DNA and T47D as targets

A water-soluble Cu (II) complex [(dien)Cu(??-1,6-DAH)Cu(dien) (NO₃)₂](NO₃)₂ has been synthesized and its effect on the carrier model DNA structure and cancer cell line proliferation was investigated. In this regard, calf thymus DNA (CT-DNA) and human breast cancer cell line, T47D, were the targets. The effect of the complex on DNA structure was investigated by means of UV/vis, fluorescence and circular dichroism (CD) spectroscopic techniques as well as dynamic light scattering (DLS), zeta potential analysis and docking assay for more analysis. The UV?Cvis absorption spectra of complex with DNA showed a slight red shift and hypochromic effect, which indicated the intercalation and electrostatic effect of complex with CT-DNA. Using ethidium bromide (EB) as a probe in fluorescence studies revealed that complex can quench the EB?CDNA fluorescence emission at different temperatures. Besides, the far UV?CCD studies displayed that the complex induces changes in the secondary structure of CT-DNA and can increase the melting temperature of DNA up to 14?°C. The DLS and zeta potential measurements confirmed the electrostatic interaction of complex with the negatively charged DNA and subsequent DNA condensation. Besides, computational studies reflect that major and minor groove binding are two modes of interaction between complex and DNA. On the other hand, growth inhibition of the complex toward T47D cell line was measured using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, which showed no cytotoxic properties.     

Fluorescence Quenching and Binding Interaction of l0-Methylacridinium Iodide to Nucleic Acids

Interaction of 10‐methylacridinium iodide (MAI) as fluorescence probe with nucleobases, nucleosides and nucleic acids has been studied by UV‐visible absorption and fluorescence spectroscopy. It was found that fluorescence of MAI is strongly quenched by the nucleobases, nucleosides and nucleic acids, respectively. The quenching follows the Stern‐Volmer linear equation. The fluorescence quenching rate constant (k_q) was measured to be 10^9‐10¹⁰ (L/mol)/s within the range of diffusion‐controlled rate limit, indicating that the interaction between MAI and nucleic acid and their precursors is characteristic of electron transfer mechanism. In addition, the binding interaction model of MAI to calf thymus DNA (ct‐DNA) was further investigated. Apparent hypochromism in the absorption spectra of MAI was observed when MAI binds to ct‐DNA. Three spectroscopic methods, which include (1) UV spectroscopy, (2) fluorescence quenching of MAI, (3) competitive dual‐probe method of MAI and ethidium bromide (EB), were utilized to determine the affinity binding constants (K) of MAI and ct‐DNA. The binding constants K obtained from the above methods gave consistent data in the same range (1.0–5.5) × 10⁴L/mol, which lend credibility to these measurements. The binding site number was determined to be 1.9. The influence of thermal denaturation and phosphate concentration on the binding was examined. The binding model of MAI to ct‐DNA including intercalation and outside binding was investigated.     

Interaction of water-soluble bridged porphyrin with DNA

A water-soluble porphyrin dimer (Por Dimer) containing eight positive charges, bridged by 4,4′-dicarboxy-2,2′-bipyridine, has been synthesized. With Meso-tetrakis(N-methyl-pyridium-4-yl)porphyrin (H₂TMPyP) as the reference compound, the water-soluble porphyrin dimer was investigated for its interaction with DNA by absorption, fluorescence, and circular dichroism (CD) spectroscopy. The apparent affinity binding constant (K _app = 1.2 × 10⁶) of Por Dimer binding to CT DNA was measured by a competition method with ethidium bromide (EB) (that of H₂TMPyP was 6.9 × 10⁶). The cleavage ability of Por Dimer to pBR322 plasmid DNA was studied by gel electrophoresis. The results suggest that the binding modes of Por Dimer were complex and involve both intercalation and outside binding. __________ Translated from Acta Chimica Sinica, 2007, 65(22): 2597–2603     

The intercalation of ethidium bromide in the chromonic lyotropic phases of drugs and nucleic acids

Chromonic liquid crystalline phases are formed by a variety of drug and dye/water systems. In contrast to conventional lyotropic phases (where micelle formation underlies the mesogenic properties), in chromonic systems the molecules stack in columns. The different chromonic phases are different arrangements of these columns. We have examined the solution of ethidium bromide (EB) in the well-documented chromonic Intal/water system. EB is a widely used nucleic acid stain which changes colour when intercalated into DNA and which becomes fluorescent.

We have charted the changes in the temperature/composition phase diagram of the Intal/water system caused by adding EB. Although there are changes in the position of the phase boundaries, the overall pattern remains qualitatively the same—implying that the host phase is accepting EB as a similar chromonic molecule. The intercalation of EB molecules in the chromonic host phase results in optical effects—a metachromic colour change and fluorescence, similar to those occurring when the dye stains DNA.

These observations strengthen our belief that the central stack of bases in DNA can be regarded as being chromonic in nature.     

Ni(II) Ternary Complex Based on Antimicrobial Drug Enoxacin: Synthesis and Biological Properties

First Ni(II) ternary complex using the quinolone antibacterial agent enoxacin (HEn) as ligand and 1,10‐phenanthroline as co‐ligand has been synthesized and characterized. It is a mononuclear structure, in which enoxacin acts as a bidentate ligand bound to the metal through the ketone oxygen and a carboxylate oxygen atom. The complex exhibited good binding propensity to human and bovine serum albumin proteins having relatively high binding constants (6.40×10⁴ and 7.12×10⁴, respectively). The investigation of the interaction of the complex with calf‐thymus (CT) DNA has been performed with UV and circular dichroism (CD) spectroscopies, indicating that they bind to CT DNA probably by the intercalative binding mode. The binding constant (K_b) of the complex with CT DNA calculated with UV is 2.03×10⁵, which is higher than that of free enoxacin drug (2.09×10⁴) and even higher than that of typical intercalation indicator (1.23×10⁵) of ethidium bromide (EB). Fluorescence competitive studies with EB have revealed that the complex exhibited the ability to displace the DNA‐bound EB using the intercalative binding site. In addition, the antimicrobial activity showed that the complex exhibited a little bit good inhibition (MIC=1.843 (g·mL^?1) against B. subtilis than free HEn.     

巯嘌呤金属配合物与小牛胸腺DNA的作用

用溴化乙锭为探针研究了巯嘌呤(mercaptopurine, MP)金属配合物与小牛胸腺 DNA的作用机制，探讨了其作用模式，即巯嘌呤与DNA是非嵌插结合，巯嘌呤金属酴 物与DNA之间的作用为静电方式和一定的嵌入方式。并求得巯嘌呤金属配合物与 DNA的结合常数。     

Mechanism of sequence-based separation of single-stranded DNA in capillary zone electrophoresis

Separation of DNA by length using CGE is a mature field. Separation of DNA by sequence, in contrast, is a more difficult problem. Existing techniques generally rely upon changes in intrinsic or induced differences in conformation. Previous work in our group showed that sets of ssDNA of the same length differing in sequence by as little as a single base could be separated by CZE using simple buffers at high ionic strength. Here, we explore the basis of the separation using circular dichroism spectroscopy, fluorescence anisotropy, and small angle X-ray scattering. The results reveal sequence-dependent differences among the same length strands, but the trends in the differences are not correlated to the migration order of the strands in the CZE separation. They also indicate that the separation is based on intrinsic differences among the strands that do not change with increasing ionic strength; rather, increasing ionic strength has a greater effect on electroosmotic mobility in the normal direction than on electrophoretic mobility of the strands in the reverse direction. This increases the migration time of the strands in the normal direction, allowing more time for the same-length strands to be teased apart based on very small differences in the intrinsic properties of the strands of different sequence. Regression analysis was used to model the intrinsic differences among DNA strands in order to gain insight into the relationship between mobility and sequence that underlies the separation.     

Intercalator-DNA interactions revealed by NIR surface-enhanced Raman spectroscopy

Using 1064 nm excited surface-enhanced Raman spectroscopy (SERS) a well known intercalator, ethidium bromide (EB), and a structurally related compound, 4-methyl-2,7-diamino-5,10-diphenyl-4,9-diazapyrenium hydrogensulfate (ADAP), have been studied. Concentration dependent SERS spectra of both aromatic species (1 × 10⁻⁷-5 × 10⁻⁵ M) indicated existence of dimeric associates at high concentration and an equilibrium shift towards monomers with a concentration decrease. Interactions of the intercalating molecules with DNA have been studied for various intercalator/DNA (base pair) molar ratios ranging from 10/1 to 1/10. In colloidal samples containing an intercalator in excess relative to DNA binding sites (from 10/1 to 2/1) enhancement of the Raman scattering gradually weakened, indicating a decrease in a number of free molecules adsorbed on the metal surface due to binding with DNA. At the drug/DNA ratios of 1/2 and 1/5 weaker but observable SERS bands indicated insertion of the drug molecules between the base pairs (intercalation strongly diminished interaction of the drug molecules with metal surface) as well as non-intercalative binding of the drug molecules able to stay in closer contact with a metal surface. A total intercalation of EB and ADAP molecules (intercalator/DNA of 1/7 and 1/10) resulted in almost complete loss of the SERS signal. Intensity of the SERS spectra of the intercalator/DNA complexes relative to the SERS intensity of the free intercalating molecules diminished to a lesser degree for ADAP/DNA than for EB/DNA. The obtained difference was attributed to a larger aromatic surface of the ADAP molecules which, although intercalated, could be positioned near the enhancing nanoparticles, unlike the smaller EB molecules which were deeply inserted within the DNA helix.     

A Programmed DNA Marker Based on Bis(4‐ethynyl‐1,8‐naphthalimide) and Three‐Methane‐Bridged Thiazole Orange

Two large conjugated naphthalimide derivatives with or without three‐methane‐bridged thiazole orange (TO3; i.e., compounds 1 a and 2 a , respectively) were designed and synthesized. The fluorescence of the naphthalimide group in compound 1 a at λ=532 nm initially decreased and that for the TO3 group at λ=655 nm increased sequentially upon adding Salmon testes (St) DNA. In contrast, without the TO3 group, the fluorescence intensity of compound 2 a monotonously decreased in response to the addition of DNA. The non‐monotonic change in the fluorescence for compound 1 a could be divided into two linear sections with two different wavelengths in the range of 0<R_{b/ 1 a} <1.2 and 1.2 <R_{b/ 1 a} <6.0 (R_{b/ 1 a} =[base pair]/[ 1 a ]). Thus, compound 1 a can be regarded as a programmed responding molecule for DNA, which can semi‐quantitatively determine the concentration of DNA over a large concentration range from the standard fluorescence curve of compound 1 a at different wavelengths when bound with DNA. Furthermore, the binding modes of compounds 1 a and 2 a with StDNA were studied by using CD spectroscopy and melting temperature (T_m) testing. The results showed that compound 1 a interacts with StDNA through multi‐interactions including weak intercalation, weak minor groove binding, and inter‐dye interactions, whereas compound 2 a bound with DNA through simultaneous intercalation and minor groove binding.     

表柔比星-铜体系与DNA作用的光谱和电化学法研究

表柔比星是临床上广泛用于治疗增殖很快的肿瘤. 应用紫外、荧光、黏度、循环伏安等方法研究了表柔比星及表柔比星-Cu^2＋体系与DNA的作用. 结果发现: 在pH＝7.4时, 表柔比星可与Cu^2＋形成稳定体系. 加入DNA后表柔比星-Cu^2＋体系的紫外吸收明显降低; Scatchard图表明表柔比星-Cu^2＋体系对溴化乙锭(EB)与DNA的结合为竞争性抑制; 同时此体系可使DNA-EB体系荧光偏振度增大; 使DNA的热变性温度(t_m)上升; 黏度增大; 循环伏安法表明DNA的加入使得表柔比星及表柔比星-Cu^2＋体系的式量电位正移; 凝胶电泳表明表柔比星-Cu^2＋体系对pBR322 DNA有非常好的水解切割活性. 综合以上结果得出: 表柔比星及表柔比星-Cu^2＋体系与DNA之间均为嵌插作用; 表柔比星-Cu^2＋体系具有更好的水解切割活性. 这些结果可为合理改善药效、降低抗癌药物毒性和设计新药提供依据.     

6-苄氨基嘌呤及其金属配合物与DNA的作用机理

新型抗癌症药剂的开发和抗癌机理研究,一直是人们争相研究的前沿课题[1-5]。而许多预防和治疗癌症的药物都是以D N A为作用靶来设计的[6]。以D N A为靶分子的金属抗癌剂,其抗癌活性是由于金属离子与D N A的配位,即金属离子与D N A的某些亲核基团(如磷酸氧位点或碱基氮、氧位点)