三齿多吡啶钴(Ⅲ)、钌(Ⅱ)配合物的合成、表征及与DNA的相互作用

合成了两种新型三齿多吡啶钴(Ⅲ) [Co(PhTPY)(H2Bzimpy)]3+(A)和钌(Ⅱ) [Ru(PhTPY)(Bzimpy)](B)混配配合物, 用元素分析和1H NMR等对其结构进行了表征, 测定了配合物B的晶体结构. 用电子吸收光谱和荧光光谱等方法研究了配合物与小牛胸腺DNA的相互作用以及配合物对pBR322DNA的断裂作用. 结果表明, 两种配合物均是通过静电作用与DNA结合的. 凝胶电泳实验结果表明, 配合物A经波长310 nm光辐射15 min, 配合物B经450 nm光辐射4 min, 可使超螺旋pBR322DNA断裂为开环缺口型和线型DNA.     

Multiple binding modes of the camptothecin family to DNA oligomers

The binding constants of camptothecin, topotecan and its lactone ring-opened carboxylate derivative to DNA octamers were measured by UV and NMR spectroscopy. The self-association of topotecan (TPT) was also measured. The carboxylate form of TPT binds in the same way as the lactone, but more weakly. Titration of TPT into d(GCGATCGC)2 shows a preferred location stacked onto the terminal G1 base. However, the intermolecular NOEs cannot be reconciled with a single conformation of the complex, and suggest a model of a limited number of conformations in fast exchange. MD calculations on four pairs of starting structures with TPT stacked onto the G1-C8 base pair in different orientations were therefore performed. The use of selected experimental "docking" restraints yielded ten MD trajectories covering a wide conformational space. From a combination of calculated free energies, NOEs and chemical shifts, some of the structures produced could be eliminated, and it is concluded that the data are consistent with two major families of conformations in fast exchange. One of these is the conformation found in a crystal of a TPT/DNA/topoisomerase I ternary complex [Proc. Natl. Acad. Sci. USA 2002, 99, 15 387-15 392].     

Topotecan dynamics,tautomerism and reactivity—1H/13C NMR and ESI MS study

Topotecan (TPT) is in clinical use as an antitumor agent, hycamtin^?. Because of this, it requires both biologically and chemically useful information to be available. TPT acts by binding to the covalent complex formed by nicked DNA and topoisomerase I. This has a poisonous effect since inserted into the single‐strand nick and TPT inhibits its religation. We used NMR to trace TPT dynamics, tautomerism and solvolysis products in various solvents and conditions. Chemical stability was assessed in methanol and DMSO as compared to water, and the regioselectivity of the N‐ and O‐methylation was studied using various alkylating agents. The reaction products of quaternization of the nitrogen atom and methylation of the oxygen atom were characterized by means of ESI MS, ¹H/¹³C‐HMBC and ‐HSQCAD NMR. We have focused on the NMR characterization of TPT with an anticipation that its aggregation, tumbling properties and the intramolecular dipolar interactions will be a common feature for other compounds described in this article. These features can also be useful in tracing the interactions of this class of topoisomerase I (TopoI) poisons with DNA. Moreover, the results explained shed light on the recently disclosed problem of lack of stability of TPT in the heart tissue homogenate samples using the analytical assays developed for this class of compounds carried out in the presence of methanol. Copyright © 2010 John Wiley & Sons, Ltd.     

三齿多吡啶钴(Ⅱ)配合物的合成、表征及其与DNA的相互作用研究

合成了两种三齿多吡啶钴(Ⅱ)配合物[Co(DMPhTPY)2]2+(ClO-4)2(A)和[Co(H2Bzimpy)2]Cl2(B),用元素分析、IR对配合物的组成和结构进行了表征,测定了配合物A的晶体结构.用电子吸收光谱、荧光光谱、循环伏安法及凝胶电泳实验等方法研究了配合物与DNA的相互作用.结果表明配合物A和B与小牛胸腺(CTDNA)的作用属部分插入和静电结合,凝胶电泳实验表明配合物A在310nm光辐射15min,可使超螺旋pBR322DNA断裂为开环缺口型和线型DNA.     

Synthesis, Characterization, DNA-binding Properties and DNA Cleavage of a New Ternary Copper(Ⅱ) Complex with Mixed-ligands of Tridentate Schiff Base and 1,10-Phenanthroline

A new copper(II) complex, [Cu(naph‐leu)phen]CH₃OH·0.5H₂O, in which naph‐leu is the tridentate Schiff base ligand derived from the condensation of 2‐hydroxy‐1‐naphthaldehyde and L‐leucine, phen is phenanthroline, has been synthesized and characterized by elemental analyses, IR spectra and single crystal X‐ray diffraction. The DNA‐binding properties of this complex have been investigated by absorption spectra, fluorescence spectra and circular dichroism (CD) spectra, as well as viscosity measurement. Results show that this copper(II) complex binds to calf thymus DNA (CT‐DNA) in an intercalative mode and its intrinsic binding constant K_b is 4.87×10³ L·mol^?1. Furthermore, the DNA cleavage activity of this copper(II) complex has also been investigated by submarine gel electrophoresis. Interestingly, it was found that this complex can cleave the supercoiled plasmid pBR322 DNA to both nicked and linear forms.     

Insight on the Interaction between the Camptothecin Derivative and DNA Oligomer Mimicking the Target of Topo I Inhibitors

The understanding of the mechanism of Topo I inhibition by organic ligands is a crucial source of information that has led to the design of more effective and safe pharmaceuticals in oncological chemotherapy. The vast number of inhibitors that have been studied in this respect over the last decades have enabled the creation of a concept of an ‘interfacial inhibitor’, thereby describing the machinery of Topo I inhibition. The central module of action of this machinery is the interface of a Topo I/DNA/inhibitor ternary complex. Most of the ‘interfacial inhibitors’ are primarily kinetic inhibitors that form molecular complexes with an “on–off” rate timing; therefore, all of the contacts between the inhibitor and both the enzyme and the DNA are essential to keep the complex stable and reduce the “off rate”. To test this hypothesis, we designed the compound using a C-9-(N-(2′-hydroxyethyl)amino)methyl substituent in an SN38 core, with a view that a flexible substituent may bind inside the nick of a model of the DNA and stabilize the complex, leading to a reduction in the “off rate” of a ligand in a potential ternary complex in vivo. Using docking analysis and molecular dynamics, free energy calculations on the level of the MM-PBSA and MM-GBSA model, here we presented the in silico-calculated structure of a ternary complex involving the studied compound 1. This confirmed our suggestion that compound 1 is situated in a groove of the nicked DNA model in a few conformations. The number of hydrogen bonds between the components of a ternary complex was established, which strengthens the complex and supports our view. The docking analysis and free energy calculations for the receptor structures which were obtained in the MD simulations of the ternary complex 1/DNA/Topo I show that the binding constant is stronger than it was for similar complexes with TPT, CPT, and SN38, which are commonly considered as strong Topo I inhibitors. The binary complex structure 1/DNA was calculated and compared with the experimental results of a complex that was in a solution. The analysis of the cross-peaks in NOESY spectra allowed us to assign the dipolar interactions between the given protons in the calculated structures. A DOSY experiment in the solution confirmed the strong binding of a ligand in a binary complex, having a K_a of 746 mM⁻¹, which was compared with a K_a of 3.78 mM⁻¹ for TPT. The MALDI-ToF MS showed the presence of the biohybrid, thus evidencing the occurrence of DNA alkylation by compound 1. Because of it having a strong molecular complex, alkylation is the most efficient way to reduce the “on–off” timing as it acts as a tool that causes the cog to brake in a working gear, and this is this activity we want to highlight in our contribution. Finally, the Topo I inhibition test showed a lower IC₅₀ of the studied compound than it did for CPT and SN38.     

Monitoring of single nicks in duplex DNA by gel electrophoretic mobility-shift assay

We demonstrate that the gel electrophoretic mobility-shift assay (EMSA) can be used for site-selective and quantitative monitoring of nicks in linear double-stranded DNA (dsDNA) thus allowing to expediently follow the nicking activity of enzymes or other agents targeted to a designated dsDNA site. At elevated temperature and/or in the presence of urea, DNA fragments carrying a single nick produced by the nicking enzyme N.BstNBI exhibit a well-detectable gel retardation effect. On the basis of permutation analysis, the decreased electrophoretic mobility of nicked dsDNA fragments is attributed to a bend (or hinge) in the DNA double helix sequence-specifically generated by a nick. Since nick-induced DNA bending depends on interaction between base pairs adjacent to a nick, the change in mobility is different for nicked DNA sites with different sequences. Therefore, EMSA monitoring of differential mobility change caused by nicks within various DNA sequences could be useful for studying the differential base stacking and nearest-neighbor energetics.     

A Novel Mononuclear Copper（Ⅱ） Complex：Crystal Structure and DNA Cleavage Ability

The reaction of N-tosylatirdine with 1,2-diaminopropane in dry benzene solution yields an intermediate H2L, N,N,N',N'-tetrakis(2-(p-tolylsulfonyl)aminoethyl) propane-1,2-diamine. The mononuclear copper(Ⅱ) complex, [CuLH2O]·H2O, was synthesized by the reaction between the intermediate and copper(Ⅱ) in absolute methanol. The complex has been characterized by IR, UV-vis and X-ray diffraction technology, and its crystal crystallizes in the orthorhombic system, space group Pbca with a = 15.589(1), b = 21.897(2), c = 27.645(2) , V = 9436.4(1) 3, Dc = 1.352 g/cm3, Z = 8, Mr = 960.68, F(000) = 4040, μ(MoKa) = 0.698 mm-1, S = 0.98, R = 0.0537 and wR = 0.1180 for 5804 observed reflections (I > 2σ(I)). In the crystal structure, a one-dimensional chain is formed by abundant hydrogen bond interactions. The interaction of the complex with DNA was monitored using agarose gel electrophoresis. The result shows that the complex can transform the supercoiled to nicked and liner forms, and has a concentration-dependent cleavage activity.     

Synthesis and photophysical evaluation of a pyridinium 4-amino-1,8-naphthalimide derivative that upon intercalation displays preference for AT-rich double-stranded DNA

The synthesis, characterisation and solid state crystal structure of a cationic 4-amino-1,8-naphthalimide derivative (1) are described. The photophysical properties of 1 are shown to vary with the solvent polarity and H-bonding ability. The fluorescence of 1 is enhanced and blue-shifted in its 1:1 complex with 5'-adenosine-monophosphate while it is partially quenched and red-shifted in its complex with 5'-guanosine-monophosphate. Linear and circular dichroism measurements show that 1 binds to double-stranded DNA by intercalation. Comparative UV-visible and fluorescence studies with double stranded synthetic polynucleotides poly(dA-dT)(2) and poly(dG-dC)(2) show that 1 binds much more strongly to the AT polymer; 1 also has a strong preference for A-T rich sequences in natural DNA. Thermal denaturation measurements also reveal a much greater stabilisation of the double-stranded poly(dA-dT)(2) than of natural DNA.     

一种新的吡咯多胺镍配合物的合成及其与DNA的作用研究

合成了一种新的吡咯-多胺金属镍配合物,并用质谱、核磁、红外、摩尔电导、元素分析等多种手段分析了配体和配合物的结构;紫外、荧光和黏度等方法分析了镍配合物与小牛胸腺DNA(CT DNA)的作用,发现配合物以插入方式与DNA结合;电泳法研究发现配合物在反应温度为50～55℃间可将超螺旋pBR 322 DNA完全切割为缺刻产物;细胞水平抗肿瘤实验表明该镍配合物具有一定的抗肝癌活性.     

DNA cleavage on photoexposure at the d-d band in ternary copper(II) complexes using red-light laser

Ternary copper(II) complexes [Cu(L1)B](ClO4) (1, 2) and [Cu(L2)B](ClO4) (3, 4), where HL1 and HL2 are tridentate NSO- and ONO-donor Schiff bases and B is a heterocyclic base, viz. dipyrido[3,2-d:2',3'-f]quinoxaline (dpq, 1 and 3) or dipyrido[3,2-a:2',3'-c]phenazine (dppz, 2 and 4), were prepared and their DNA binding and photoinduced DNA cleavage activity studied. Complex 1, structurally characterized by single-crystal X-ray crystallography, shows an axially elongated square-pyramidal (4 + 1) coordination geometry in which the monoanionic L1 binds at the equatorial plane. The NN-donor dpq ligand exhibits an axial-equatorial binding mode. The complexes display good binding propensity to calf thymus DNA, giving a relative order 2 (NSO-dppz) > 4 (ONO-dppz) > 1 (NSO-dpq) > 3 (ONO-dpq). They cleave supercoiled pUC19 DNA to its nicked circular form when treated with 3-mercaptopropionic acid (MPA) by formation of hydroxyl radicals as the cleavage active species under dark reaction conditions. The photoinduced DNA cleavage activity of the complexes was investigated using UV radiation of 365 nm and red light of 633, 647.1, and 676.4 nm (CW He-Ne and Ar-Kr mixed gas ion laser sources) in the absence of MPA. Complexes 1 and 2, having photoactive NSO-donor Schiff base and dpq/dppz ligands, show dual photosensitizing effects involving both the photoactive ligands in the ternary structure with significantly better cleavage properties when compared to those of 3 and 4, having only photoactive dpq/dppz ligands. Involvement of singlet oxygen in the light-induced DNA cleavage reactions is proposed. A significant enhancement of the red-light-induced DNA cleavage activity is observed for the dpq and dppz complexes containing the sulfur ligand when compared to their earlier reported phen (1,10-phenanthroline) analogue. Enhancement of the cleavage activity on photoexposure at the d-d band indicates the occurrence of metal-assisted photosensitization processes involving the LMCT and d-d band in the ternary structure.     

Can an ancillary ligand lead to a thermodynamically stable end-on 1 : 1 Cu-O2 adduct supported by a beta-diketiminate ligand?

The finding that dioxygen binds end-on to the Cu(B) site in the crystal structure of a precatalytic complex of peptidylglycine alpha-hydroxylating monooxygenase has spurred the search for biomimetic model complexes exhibiting the same dioxygen coordination. Recent work has not only indicated that sterically hindered beta-diketiminate ligands (L(1)) could support side-on 1 : 1 Cu-O(2) adducts, but also that an end-on L(1)Cu(THF)O(2) structure occurs as an unstable intermediate in the oxygenation mechanism of the Cu(I) complex. In this work, density functional theory and multireference methods are used to determine the potential of ancillary ligands, X, other than THF to yield thermodynamically stable end-on L(1)CuXO(2) species. A diverse set of ligands X, comprising phosphines, thiophene, cyclic ethers, acetonitrile, para-substituted pyridines, N-heterocyclic carbenes, and ligands bearing hydrogen bond donors, has been considered in order to identify ligand characteristics which energetically favor end-on L(1)CuXO(2) over: a) reversion to the Cu(I) complex and dioxygen, b) isomerization to side-on L(1)CuXO(2), and c) decay to L(1)CuO(2) and X. Ancillary ligands with judiciously chosen degrees and orientation of steric bulk and which bear potential hydrogen bond donors to an end-on bound dioxygen moiety most favor oxygenation of L(1)CuX to yield end-on L(1)CuXO(2). Conversion to the side-on isomer can be deterred through the use of a sufficiently bulky ligand X, such as one that is at least the size of a 5-membered ring. Loss of X to give L(1)CuO(2) can be made prohibitively endergonic by employing ligands X which are highly electron donating and which backbond strongly with and sigma-donate significantly to copper.     

双核铜(Ⅱ)配合物{[Cu(Phen)(Nap)_2]_2·(EtOH)_2·(H_2O)_2}(Phen=1,10-菲咯啉,Nap=1-萘甲酸,EtOH=乙醇)的合成、晶体结构及性质

合成了一种新型的配合物{[Cu(Phen)(Nap)_2]_2·(EtOH)_2·(H_2O)_2}(Phen=1,10-菲咯啉,Nap=1-萘甲酸,EtOH=乙醇)。通过元素分析、红外光谱、热重等测试技术对其进行了表征,同时用X射线单晶衍射确定了其晶体结构,其配合物为双核铜结构。利用循环伏安法和发射光谱研究了该配合物的电化学和发光性能;采用紫外光谱和荧光光谱法研究了配合物与小牛胸腺DNA(ct-DNA)的相互作用。结果表明,配合物为不可逆氧化还原过程,其荧光发射光谱为416 nm,与小牛胸腺DNA(ct-DNA)以沟面结合方式相互作用,配合物结合常数Kb1=4.68×10~3L/mol。     

Synthesis of a New Cobalt (II) Complex and its Interaction with DNA

The interaction of metal complexes with DNA has been widely studied by differentmethods such as spectrophotometry, light scattering technique, fluorometry1-3. Manycomplexes such as Co(phen)2 ,Co(en)2 ,Fe(EDTA)2- etc.4,5 have been synthesized and 3+ 3+their effect on DNA has been studied in order to further explain the mechanism of genemutation, anti-cancer or cancer-induced reason and DNA targeted drugs. In this paper,a new cobalt complex was synth…     

4-氯-2-(1H-咪唑并[4,5-f][1,10]菲咯啉)苯酚铜(Ⅱ)配合物的晶体结构及其与DNA的相互作用

利用菲咯啉酮衍生物4-氯-2-(1H-咪唑并[4,5-f][1,10]菲咯啉)苯酚(HL)设计合成了一种新的单核铜配合物[Cu(L)(5-Cl-sal)(DMF)]ClO_4·DMF(5-Cl-Hsal=5-氯-水杨醛),用元素分析和X射线单晶衍射等手段对配合物进行了表征。该配合物晶体属三斜晶系,P1空间群。用紫外吸收光谱、荧光光谱和凝胶电泳等方法研究了配合物与DNA的相互作用。结果表明,配合物以插入方式与CT-DNA结合,结合常数为1.02×10~3 L·mol~(-1)。同时配合物也能较大程度淬灭EB-DNA复合物的荧光,表观键合常数为4.37×10~5L·mol_(-1),略小于经典键合常数107 L·mol~(-1)。淬灭机理为动态淬灭。凝胶电泳实验研究表明配合物在H_2O_2存在下可将pBR322质粒DNA切割为开环缺口型DNA和线型DNA,配合物浓度越大,切割效果越好。机理研究显示,配合物切割DNA的反应是由羟基自由基(·OH)和单线态氧(~1O_2)作为活性物种的氧化切割过程。     

Crystal structure and DNA interaction of a nickel(II) complex with N-benzyl-N ′-[2-(benzylamino)ethyl]ethane-1,2-diamine

N-Benzyl-N′-[2-(benzylamino)ethyl]ethane-1,2-diamine was prepared by reduction of its Schiff base analog. Its Ni(II) complex was synthesized and characterized. The crystal structure of the complex showed a square pyramidal structure in which a chlorine atom bridges two Ni(II) atoms in the common apical position. The dinuclear complex has two identical five-coordinate Ni(II) atoms. Interaction of the complex with calf thymus DNA was investigated by UV spectroscopy and fluorescence spectroscopy, and the results suggest that the complex binds to DNA by electrostatic interactions only. The binding constant is 1.02 × 10⁴ mol⁻¹ L.     

Bis(dipyridophenazine)copper(II) complex as major groove directing synthetic hydrolase

The copper(II) complex [Cu(dppz)(2)Cl]Cl () has been prepared, structurally characterized and its DNA binding and cleavage properties studied (dppz, dipyridophenazine). Crystal structure of 1xdppzxH(2)O shows the presence of the monocationic copper(II) complex containing two dppz ligands and one chloride in the five coordinate structure. While one bidentate chelating dppz ligand occupies the basal plane, the other dppz ligand shows an axial/equatorial mode of bonding. The chloride ligand binds at the basal plane. The complex crystallizes with dppz and water as lattice molecules. The dppz moieties in the metal-bound and free forms are involved in pi-pi stacking interactions. The one-electron paramagnetic complex shows a visible spectral d-d band at 707 nm in DMF and displays quasireversible cyclic voltammetric response for the Cu(II)/Cu(I) couple near 0.1 V vs. SCE in DMF-0.1 M TBAP. The complex which is an avid binder to calf thymus DNA giving a binding constant (K(b)) value of 2.0 x 10(4) M(-1) in DMF-Tris buffer, cleaves supercoiled pUC19 DNA in an oxidative manner in the presence of mercaptopropionic acid (MPA) as a reducing agent or on photo irradiation at 312 nm. Control experiments show major groove binding and DNA cleavage via the formation of hydroxyl radical in the presence of MPA and by singlet oxygen in the photocleavage reaction. The complex exhibits significant hydrolytic cleavage of DNA in the dark in the absence of any additives at a rate of approximately 3.0 h(-1). The hydrolytic nature of the DNA cleavage is evidenced from the T4 ligase experiments converting the nicked circular form to its original supercoiled form quantitatively. Complex presents a rare example of copper-based major groove directing efficient synthetic hydrolase.     

4-氯-2-(1H-咪唑并[4,5-f][1,10]菲咯啉)苯酚铜(Ⅱ)配合物的晶体结构及其与DNA的相互作用

利用菲咯啉酮衍生物4-氯-2-(1H-咪唑并[4,5-f][1,10]菲咯啉)苯酚(HL)设计合成了一种新的单核铜配合物[Cu (L)(5-Cl-sal)(DMF)]ClO₄·DMF (5-Cl-Hsal=5-氯-水杨醛),用元素分析和X射线单晶衍射等手段对配合物进行了表征。该配合物晶体属三斜晶系,P1空间群。用紫外吸收光谱、荧光光谱和凝胶电泳等方法研究了配合物与DNA的相互作用。结果表明,配合物以插入方式与CT-DNA结合,结合常数为1.02×10³ L·mol^-1。同时配合物也能较大程度淬灭EB-DNA复合物的荧光,表观键合常数为4.37×10⁵ L·mol^-1,略小于经典键合常数10⁷ L·mol^-1。淬灭机理为动态淬灭。凝胶电泳实验研究表明配合物在H₂O₂存在下可将pBR322质粒DNA切割为开环缺口型DNA和线型DNA,配合物浓度越大,切割效果越好。机理研究显示,配合物切割DNA的反应是由羟基自由基(·OH)和单线态氧(¹O₂)作为活性物种的氧化切割过程。     

Nd(Ⅲ)与Hbbimp配合物的合成及其与DNA的作用研究

合成并表征了新的双核配合物[Nd₂(bbimp)(CH₃COO)(CH₃CH₂O)₂(CH₃CH₂OH)](ClO₄)₂,Hbbimp=2,6-二[二(2-苯并咪唑甲基)]氨甲基-4-甲基苯酚.用光谱学手段研究了配合物与小牛胸腺(CT)DNA的作用,结果表明,配合物使CT的DNA最大吸收峰发生减色和红移;使溴化乙锭(EB)-DNA复合物体系荧光强度减弱;热变性实验表明配合物使DNA的变性过程和降解过程共存.在50℃,pH=8.0时,单独的配合物对超螺旋质粒pBR322DNA的断裂的效果最好,可将大部分超螺旋DNA(CCC带)转化为缺刻产物(OC带);当c(H₂O₂)<1×10^-3mol/L,n(配合物):n(H₂O₂)=1:20时,配合物在较低浓度时即可将CCC带全部转化为OC带.     

Double-strand hydrolysis of plasmid DNA by dicerium complexes at 37 degrees C.

Significant effort has been made to develop synthetic metal complexes that hydrolyze DNA. Here we report a new dicerium complex, Ce(2)(HXTA) (HXTA = 5-methyl-2-hydroxy-1,3-xylene-alpha,alpha-diamine-N,N,N',N'-tetraacetic acid), which can hydrolyze DNA at pH 8 and 37 degrees C. This complex hydrolyzes DNA restriction fragments to give products with high regioselectivity, affording >90% 5'-OPO(3) and 3'-OH ends, like the products of DNA hydrolyzing enzymes. Ce(2)(HXTA) also hydrolyzes Litmus 29 plasmid DNA to afford both nicked and linear DNA. Analysis of the relative amounts of supercoiled, nicked, and linear DNA present show that there is one double-strand cleavage per ten single-strand cleavages, indicating that the linear DNA formed cannot be the result of two random single-strand cleavage events. The kinetics of nicked and linear DNA formation are comparable, both being associated with apparent first-order rate constants of approximately 1 x 10(-)(4) s(-)(1) for complex concentrations of 10(-)(5)-10(-)(4) M. These observations suggest that similar factors affect the hydrolysis of the first and second DNA strands and that cleaving the phosphodiester bond is likely the rate determining step in both cases. This is the first detailed study of a metal complex shown to mimic DNA hydrolases in their capability to effect double-strand DNA hydrolysis regioselectively at the 3'-O-P bond.