DNA cleavage promoted by Cu2+ complex of cyclen containing pyridine subunit

The tetraazamacrocycle crown ether (cyclen) containing two pyridine subunits was prepared by a modified procedure and the interaction of its metal complexes with DNA was studied by agarose gel electrophoresis analysis. The results indicate that the Cu²⁺ complex as nuclease model can promote the hydrolysis of phosphodiester bond of supercoiled DNA. The rate of degradation of the supercoiled DNA (form I) to nicked DNA (form II) obtained at physiological condition in the presence of 2.14 mM Cu²⁺ complex is 2.31 × 10^–3 min⁻¹. The dependence of the rate of supercoiled DNA cleavage from the complex concentration shows an unusual profile and a hydrolytic cleaving mechanism of two monometallic complexes through cooperation from two-point binding to DNA is proposed.

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Graphical abstract DNA cleavage promoted by metal complex of cyclen containing pyridine subunit Ying Li, Xiao-Min Lu, Xin Sheng, Guo-Yuan Lu*, Ying Shao and Qiang Xu* The copper complex of tetraazamacrocycle crown ether (cyclen) containing two pyridine subunits can promote the hydrolysis of phosphodiester bond of supercoiled DNA and a hydrolytic mechanism of two monometallic complexes through cooperation from two-point binding to DNA is proposed.

     

Resolution of circular, nicked circular and linear DNA, 4.4 kb in length, by electrophoresis in polyacrylamide solutions.

Circular DNA of more than 1,400 bp in size is known not to migrate into polyacrylamide gels. The migration of supercoiled plasmid pBR322 DNA (4,363 by) into uncrosslinked polyacrylamide (Mw 5 x 10(6)) solutions and its separation, on the basis of conformation, from its nicked form is demonstrated in this study. Migration of the supercoiled, nicked circular and linear forms of the plasmid DNA is retarded in proportion to the concentration of uncrosslinked polyacrylamide, the degree of retardation being highest for the nicked circular form. Decreasing the level of supercoiling of the covalently closed circular form by decreasing the concentration of the intercalating dye (ethidium homodimer) shows that the degree of retardation decreases in proportion to the superhelix density.     

Cytotoxic copper(II) complex of tripyridoquinoxaline with DNA hydrolase activity

A monomeric copper(II) complex, [Cu(tpq)₂(H₂O)₂](ClO₄)₂, (tpq = tripyridoquinoxaline), has been synthesized and characterized spectroscopically. This complex has been found to bind DNA intercalatively and the DNA binding constant, K_b, for this complex has been determined from absorption measurements and was found to be (5.7 ± 0.3) × 10³ M⁻¹. This complex successfully promotes hydrolytic cleavage of plasmid DNA, producing single and double DNA strand breaks in the absence of any added cofactor. The amount of conversion of the supercoiled form of plasmid to the nicked circular form depends on the concentration of the copper complex as well as the duration of the incubation of the complex with DNA. The rate of conversion of SC to NC has been determined to be 2.65 × 10⁻⁴ s⁻¹ at pH 7.2 in the presence of 80 μM of the complex. This complex has also been shown to be cytotoxic towards A549 lung adenocarcinoma cells. This complex has been shown to bring about apoptosis of the cancerous A549 cell line.     

Sequence-selective and hydrolytic cleavage of DNA by zinc finger mutants

We have reported the successful conversion of the structural zinc site in zinc finger peptides to a functional zinc site. A series of resulting zinc finger mutants exhibit the hydrolytic ability of the activated ester depending on the coordination geometry and acidity of the zinc ions. In this study, we explored the hydrolytic ability of DNA by the H4 mutant since the mutant showed the highest hydrolytic ability of the activated ester among the series of mutant peptides. The zinc-bound form of the H4 mutant peptide exhibited the hydrolytic ability of activated phosphoesters and even converted the supercoiled plasmid to the nicked circular form. An increasing ionic strength leads to a loss in the nuclease ability of the zinc finger mutants due to the nonspecific interaction between the zinc finger peptide and DNA. In sharp contrast, the three-tandem H4-type zinc finger protein performed the specific DNA hydrolysis at the GC box even at a high ionic strength. Thus, the present study demonstrated that converting the native zinc site to the hydrolytic zinc site in the zinc finger protein is a novel approach for creating artificial nucleases with sequence selectivity.     

Electrophoretic behavior of plasmid DNA in the presence of various intercalating dyes

In the present study, the electrophoretic behavior of linear, supercoiled and nicked circular plasmid DNA in the presence of various intercalating dyes was characterized using pGL3 plasmid DNA as a model. The enzymatic digestion of pGL3 plasmid DNA with HindIIIwas monitored by capillary electrophoresis coupled with laser-induced fluorescence detection (CE-LIF). Nicked circular plasmid DNA was found to be relatively sensitive to enzymes, and was almost digested into the linear conformer after 10-min incubation, indicating that nicked circular plasmid DNA has little chance of targeting and entering the cell nucleus. Partly digested plasmid DNA containing only linear and supercoiled conformers can be used as a standard to confirm the migration order of plasmid DNA. In methylcellulose (MC) solution with YO-PRO-1 or YOYO-1, linear plasmid DNA eluted first, followed by supercoiled and nicked plasmid DNA, and nicked plasmid DNA eluted as a broad peak. With SYBR Green 1, nicked plasmid DNA eluted first as three sharp peaks, followed by linear and supercoiled plasmid DNA. The nuclear plasmid DNA from two transfected cell lines was successfully analyzed using the present procedure. Similar results were obtained with an analysis time of seconds using microchip electrophoresis with laser-induced fluorescence detection (mu-CE-LIF). To our knowledge, these results represent the first reported analysis of nuclear plasmid DNA from transfection cells by CE-LIF or mu-CE-LIF without pre-preparation, suggesting that the present procedure is a promising alternative method for evaluating transfection efficiency of DNA delivery systems.     

Efficient plasmid DNA cleavage by a mononuclear copper(II) complex

The Cu(II) complex of the ligand all-cis-2,4,6-triamino-1,3,5-trihydroxycyclohexane (TACI) is a very efficient catalyst of the cleavage of plasmid DNA in the absence of any added cofactor. The maximum rate of degradation of the supercoiled plasmid DNA form, obtained at pH 8.1 and 37 degrees C, in the presence of 48 microM TACI.Cu(II), is 2.3 x 10(-3) s(-1), corresponding to a half-life time of only 5 min for the cleavage of form I (supercoiled) to form II (relaxed circular). The dependence of the rate of plasmid DNA cleavage from the TACI.Cu(II) complex concentration follows an unusual and very narrow bell-like profile, which suggests an high DNA affinity of the complexes but also a great tendency to form unreactive dimers. The reactivity of the TACI.Cu(II) complexes is not affected by the presence of several scavengers for reactive oxygen species or when measured under anaerobic conditions. Moreover, no degradation of the radical reporter Rhodamine B is observed in the presence of such complexes. These results are consistent with the operation of a prevailing hydrolytic pathway under the normal conditions used, although the failure to obtain enzymatic religation of the linearized DNA does not allow one to rule out the occurrence of a nonhydrolytic oxygen-independent cleavage. A concurrent oxidative mechanism becomes competitive upon addition of reductants or in the presence of high levels of molecular oxygen: under such conditions, in fact, a remarkable increase in the rate of DNA cleavage is observed.     

Arm effects of mononuclear armed cyclen copper complexes on DNA cleavage

Novel cyclen copper(II) complexes appending different side arms were synthesized as DNA cleavage agents. Both the intermediates and mononuclear complexes were characterized by ¹H NMR, ESI-HRMS, Elemental analyses and IR, and their catalytic activities for DNA cleavage and DNA binding abilities were investigated. The results indicate that the copper(II) complexes could catalyze the cleavage of supercoiled DNA (pUC 19 plasmid DNA) under physiological conditions to produce nicked DNA with high yields (nearly 100%) via an oxidative mechanism in the absence of exogenous agents; The copper complex bearing an 9-anthryl group gave superior DNA interactions to those bearing phenyl or methyl groups.     

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.     

Synthesis, structure and nuclease activity of copper complexes of disubstituted 2,2′-bipyridine ligands bearing ammonium groups

A series of Cu(II) complexes of disubstituted 2,2′-bipyridine bearing ammonium groups [Cu(L¹⁻⁴)₂Br]⁵⁺ (1–4, L¹ = [5,5′-(Me₂NHCH₂)₂-bpy]²⁺, L² = [5,5′-(Me₃NCH₂)₂-bpy]²⁺, L³ = [4,4′-(Me₂NHCH₂)₂-bpy]²⁺, L⁴ = [4,4′-(Me₃NCH₂)₂-bpy]²⁺ and bpy = 2,2′-bipyridyl) were synthesized, of which complexes 1 and 4 were structurally characterized. Both coordination configurations of Cu(II) ions can be described as distorted trigonal bipyramid. The interaction between all complexes and CT-DNA was evaluated by thermal-denaturation experiments and CD spectroscopy. Results show that the complexes interact with CT-DNA via outside electrostatic interactions and their binding ability follows the order: 1 > 2 > 3 > 4. In the absence of any reducing agents, the cleavage of plasmid pBR322 DNA by these complexes was investigated and the hydrolysis kinetics of DNA was studied in Tris buffer (pH 7.5) at 37 °C. Obtained pseudo-Michaelis–Menten kinetic parameters: 15.0, 13.6, 2.01 and 1.69 h⁻¹ for 1, 2, 3 and 4, respectively, indicate that complexes 1 and 2 exhibit very high DNA cleavage activities. According to their crystal data, the high nuclease activity may be attributed to the strong interaction of the metal moiety and two ammonium groups with phosphate groups of DNA.     

壳聚糖季铵盐-Zn(Ⅱ)催化磷酸双酯与质粒DNA水解动力学

采用壳聚糖与缩水甘油三甲基氯化铵反应制备了壳聚糖季铵盐(HTACC), 研究了其Zn(Ⅱ)配合物HTACC-Zn(Ⅱ)催化DNA的模拟底物对硝基苯酚磷酸双酯(BNPP)水解的动力学过程及其对质粒DNA的催化裂解. 结果表明, HTACC-Zn(Ⅱ)对BNPP的水解反应具有良好的催化活性, 其表观一级速率常数可达到6.7×10-6 s-1, 为BNPP自发水解时的6.0×104倍; 同时, HTACC-Zn(Ⅱ)还能够有效催化质粒DNA(pUC19)的裂解, 使DNA分子由超螺旋结构裂解为开环和线型结构.     

缬氨酸Schiff碱金属铜配合物对质粒DNA的切割作用

缬氨酸Schiff碱金属铜配合物(PBP-L-Val-Cu)是新合成的一类非酶类切割工具, 合成了4种类型样品分别为L-CH3 Cu, D-CH3 Cu, L-Ph Cu和D-Ph Cu. 以质粒DNA(pUC18)为材料,分别对这4种类型化合物进行核酸切割效率的研究, 得出适合的反应体系后, 通过琼脂糖凝胶电泳对反应不同时间后核酸切割产物进行检测, 最终分别得到每种化合物将超螺旋型DNA切割成为开环型DNA和直线型DNA的切割效率, 经比较得出L-CH3 Cu型的切割效率是最快的. 将直线型DNA切割产物用琼脂糖凝胶回收试剂盒进行回收, 得到的直线型切割产物可以在T4连接酶的作用下重新连接起来. 利用酶切法对切口进行检测, 结果表明, 切割作用是具有特异性的. 另外, 该化合物对质粒pNQ216也具有切割活性.     

Crystal structures and DNA cleavage activities of two mononuclear nickel(II) complexes

Two new nickel complexes, [Ni(L₁)₂]?·?2(CH₃OH) (1) and [Ni(L₂)₂]?·?2(CH₃OH) (2), where HL₁ is 4-chloro-2-((2-hydroxy-ethylimino)methyl)phenol and HL₂ is 4-fluoro-2-((2-hydroxy-ethylimino)methyl)phenol, have been synthesized and characterized by single-crystal X-ray diffraction and UV-Vis absorption spectra. The coordination polyhedron of nickel(II) in each complex can be described as distorted octahedral. The interactions between the complexes and calf thymus (CT)-DNA/DNA were investigated by UV-Vis spectra and agarose gel electrophoresis. The results show that the complex transforms supercoiled to nicked form and exhibits effective DNA cleavage activity via hydrolytic cleavage mechanism.     

Investigation of DNA cleavage activities of new oxime-type ligand complexes and molecular modeling of complex-DNA interactions

Nucleolytic activities of some new oxime-type ligand complexes were investigated by neutral agarose gel electrophoresis. Analysis of the cleavage products in agarose gel indicated that all complexes used converted supercoiled pUC18 plasmid DNA to its nicked or linear form. It was found that nucleolytic activities of the complexes depend on the complex concentration, reaction time and the presence of a cooxidant (magnesium monoperoxyphthalate, MMPP) in the reaction mixture. However, the complexes cleaved pUC18 plasmid DNA at all investigated pH values. Nucleolytic activities of complexes were investigated for different complex concentrations (0.1–100 μmol L⁻¹), pH values (6.0–10.0) and reaction times (0–60 min). Molecular modeling studies performed by the Hyperchem Software together with DNA-binding studies showed that planar sites of the complexes intercalated into double stranded DNA. It can be concluded that all oxime-type ligand complexes used can be evaluated as nuclease mimics.     

Synthesis,DNA-binding,and Photocleavage of 2,3-Di-2-pyridylquinoxaline-silver（I） Complex

A new dinuclear complex, [Ag（L）（CH3CN）]2（ClO4）2·2H2O（L=2,3-di-2-pyridylquinoxaline）, was prepared and characterized by elemental analyses, IR spectroscopy, and single-crystal X-ray diffraction analyses. The interaction of the complex with calf thymus DNA（CT-DNA） was investigated by absorption, fluorescence spectroscopies, and viscosity measurement. The results suggested that the complex was bound to DNA via an intercalative mode. The intrinsic binding constant value Kb was found to be approximately 1.48×10^3 L·mol^-1. Moreover, the Ag（I） complex could cleave the plasmid pUC19 DNA from the supercoiled Form Ⅰto the nicked FormⅡ under irradiation at 365 nm.     

Synthesis,DNA binding,nuclease activity and cytotoxic studies of a wheel‐shaped octanuclear copper(II) complex based on 1,2,4‐triazole

The antitumor activity shown by many platinum complexes has produced a strong interest in research of new organometallic compounds. Among the metal compounds synthesized and tested, copper compounds have received considerable attention because of their cytotoxic activity against solid tumors. A novel wheel‐shaped octanuclear copper(II) complex with a 1,2,4‐triazole derivative ligand formulated as [Cu₈L₄](ClO₄)₈?11H₂O ( 1 ) (L = 3,5‐bis((bis(2‐hydroxylethyl)amino)methyl)‐4 H‐1,2,4,‐triazole‐4‐amine) has been synthesized and structurally characterized. In 1 , eight Cu atoms are linked through 1,2,4‐triazole units and alkoxide bridges to form a centrosymmetric octanuclear Cu(II) metallomacrocycle. The interaction of complex 1 with calf thymus DNA has been studied using UV absorption, fluorescence and circular dichroism spectroscopies, viscosity measurements and cyclic voltammetry. The apparent binding constant (k_app) value for 1 is 1.59 × 10⁵ M^?1. Furthermore, complex 1 displays efficient oxidative cleavage of supercoiled DNA in the presence of external agents, the rate constant for the conversion of supercoiled to nicked DNA being 2.67 × 10^?5 s^?1. Interestingly, cytotoxicity studies on the MCF‐7 human breast cancer cell line show that the IC₅₀ value of 1 is less than that of cisplatin for the same cell line, revealing that it has the potential to act as an effective metal‐based anticancer drug. Copyright © 2016 John Wiley & Sons, Ltd.     

两个4,4'-二甲基-2,2'-联吡啶锰(Ⅱ)配合物切割DNA的动力学研究

对2个4,4'-二甲基-2,2'-联吡啶锰(Ⅱ)配合物在生理条件及H2O2的存在下对DNA切割的动力学进行了研究.结果表明,这2个配合物分别存在下的DNA切割反应具有相似的动力学反应特征.其中对超螺旋DNA切割成缺口DNA步骤,均表现为三级反应,即反应速率分别与底物DNA的浓度、配合物的浓度和H2O2的浓度的一次方成正比;同时得到了2个反应的速率常数、活化能(Ea)、活化焓(△H≠)和活化熵(△S≠)等动力学参数,并根据这些结果提出了一个可能的氧化切割反应机理.     

Vesicles and micelles from amphiphilic zinc(II)-cyclen complexes as highly potent promoters of hydrolytic DNA cleavage

Phosphate esters are essential to any living organism and their specific hydrolysis plays an important role in many metabolic processes. As phosphodiester bonds can be extraordinary stable, as in DNA, great effort has been put into mimicking the active sites of hydrolytic enzymes which can easily cleave these linkages and were often found to contain one or more coordinated metal ions. With this in mind, we report micellar and vesicular Zn(II)-cyclen complexes which considerably promote the hydrolytic cleavage of native DNA and the activated model substrate bis(4-nitrophenyl)phosphate (BNPP). They are formed by self-assembly from amphiphilic derivatives of previously employed complexes in aqueous solution and therefore allow a simple and rapid connection of multiple active metal sites without great synthetic effort. Considering the hydrolytic cleavage of BNPP at 25 °C and pH 8, the micellar and vesicular metal catalysts show an increase of second-order rate constants (k(2)) by 4-7 orders of magnitude compared to the unimolecular complexes under identical conditions. At neutral pH, they produce the highest k(2) values reported so far. For pBR322 plasmid DNA, both a conversion of the supercoiled to the relaxed and linear form, and also a further degradation into smaller fragments by double strand cleavages could be observed after incubation with the vesicular Zn(II)-complexes. Finally, even the cleavage of nonactivated single-stranded oligonucleotides could be considerably promoted compared to background reaction.     

DNA-binding and photoactivated cleavage of enantiomeric ruthenium(II) complexes

A set of enantiomeric Ru^II complexes Δ- and Λ-[Ru(bpy)₂TAPTP](PF₆)₂(bpy=2,2’-bipyridine, TAPTP=4,5,9,18-tetraazaphenanthreno[9,10-b]triphenylene) have been synthesized and characterized. Binding of both enantiomers to calf thymus DNA has been studied by spectroscopic methods, viscosity, and equilibrium dialysis. The experimental results indicated that both enantiomers bind to DNA by intercalation. Upon irradiation at 302 nm, both enantiomers were found to promote the cleavage of plasmid pBR 322 DNA from supercoiled form I to a nicked form II, and obvious enantioselectively was observed on DNA cleavage, the Λ- enantiomer exhibiting higher cleaving efficiency. The mechanisms for DNA cleavage by the two enantiomers are also proposed.     

Rapid analysis of a plasmid by hydrophobic-interaction chromatography with a non-porous resin

A HPLC technique has been developed, based on hydrophobic-interaction Chromatography with a non-porous packing (TSKgel Butyl-NPR, Tosoh Biosep LLC), that allows separation of the open circular (nicked) and supercoiled forms of five DNA plasmids, ranging in size from 4 to 30 kilo base pairs (kb). The identity of the bands was determined through light scattering and gel electrophoresis. Several buffers, gradients, flow-rates and temperatures were evaluated in determining the optimum operating conditions for the separation. For all plasmids a reversed ammonium sulfate in phosphate buffer (pH 7.1) gradient was established. The chromatographic resolution between the supercoiled and nicked peaks was found to be a function of flow-rate and temperature. The resolution and the elution order did not vary with plasmid size, with the open-circular form always being eluted before the supercoiled form. Hydrophobic-interaction chromatography is a useful alternative to ion exchange or size exclusion for the chromatography of large plasmids, up to 30 kb.     

Ternary complexes of cobalt cysteinylglycine with histidylserine and histidylphenylalanine-stabilities and DNA cleavage properties

Interaction of cobalt cysteinylglycine with histidylserine and histidylphenylalanine was investigated in a 1 : 1 : 1 ratio at 35°C and 0·10 mol dm⁻³ ionic strength. Their stabilities and geometries were determined. Their DNA binding and cleavage properties were investigated. The intrinsic binding constants (K _b ) for DNA bound 1 and 2 (3·03 × 10³ M⁻¹ for 1 and 3·87 × 10³ M⁻¹ for 2) were determined. Even though the negative charge on the complexes reduced their affinity for DNA, there was an enhancement of binding through specificity. The degradation of plasmid DNA was achieved by cobalt dipeptide complexes [Co^II(CysGly)(HisSer)] (1) and [Co^II(CysGly)(HisPhe)] (2). Cleavage experiments revealed that 1 and 2 cleave supercoiled DNA (form I) to nicked circular (form II) through hydrolytic pathway at physiological pH. The DNA hydrolytic cleavage rate constants for complexes 1 and 2 were determined to be 0·62 h⁻¹, for 1 and 0·38 h⁻¹ for 2 respectively.