DNA Binding and Oxidative Cleavage by a Water-soluble Carboxyl Manganese（Ⅲ） Corrole

The interaction of calf thymus DNA （CT DNA） and water-soluble manganese corrole, 5,10,15-tris（4-carboxyphenyl）corrolatomanganese（Ⅲ） （MnuTCPC） has been studied by absorption spectra, fluorescence spectra and CD spectra, as well as by viscosity measurements. Results revealed that this manganese corrole binds to CT DNA via an outside groove binding mode with intrinsic binding constant Ku of 4.67 × 104 Lomol L DNA cleavage activities of MnmTCPC in the presence of various oxidants were also investigated, MnmTCPC can cleave the supercoiled plas- mid pBR322 DNA to both nicked and linear form in the presence of hydrogen peroxide or tert-BuOOH, while no nuclease activity was observed by using KHSO5 as oxidant. Inhibitor tests revealed that hydroxyl radicals or singlet oxygen was not involved in MnTCPC mediated DNA oxidative cleavage. It is suggested that （oxo）manganese（V） corrole is the possibly active intermediate in this oxidative cleavage reactions.     

新型有机小分子DNA切割试剂的合成

根据活性基团的协同催化原理,设计合成了有机小分子核酸切割剂1-(N-胍乙基)-4-(N-羟乙基)哌嗪盐酸盐(4),并通过核磁共振和液相色谱-质谱联用技术对其结构进行了表征.利用琼糖凝胶电泳研究了pH值对其切割pUC 19 DNA效率的影响,通过自由基猝灭实验研究其切割DNA的反应类型.运用密度泛函理论,利用Gaussian软件进行了理论计算,研究其裂解DNA的反应方式.研究结果表明,在pH=7.2时化合物4的裂解效率最高,且能通过非氧化还原反应以磷酯转移的方式裂解DNA的磷酸二酯键.     

Quantitative footprinting analysis of drug-DNA interactions: Fe(III) methidium-propyl-EDTA as a probe

Quantitative footprinting studies involving a 139-base pair restriction fragment from pBR322 DNA, a lexitropsin ligand and two different DNA cleavage agents, the enzyme DNase I and the footprinting reagent Fe(III) methidium-propyl-EDTA (Fe-MPE), are described. The autoradiographic data showed that the ligand, an analogue of netropsin possessing two N-methylimidazole groups, binds to four regions on the 139-mer which are rich in GC. Analysis of the data leading to individual binding constants for each of the four loading events on the 139-mer revealed that Fe-MPE and DNase I report the same binding constants for the lexitropsin bound to its interaction sequences. The fact that the data from both probes can be analyzed using a common model indicates that the DNA cleavage specificity of the probe and not its binding/cleavage mechanism is the important factor in reporting of site loading information in the footprinting experiment. The study also showed that under certain conditions it is possible to gain information on the density of ligand binding sites on carrier DNA by monitoring site loading events on the labeled fragment.     

Aliphatic peptidyl hydroperoxides as a source of secondary oxidation in hydroxyl radical protein footprinting

Hydroxyl radical footprinting is a technique for studying protein structure and binding that entails oxidizing a protein system of interest with diffusing hydroxyl radicals, and then measuring the amount of oxidation of each amino acid. One important issue in hydroxyl radical footprinting is limiting amino acid oxidation by secondary oxidants to prevent uncontrolled oxidation, which can cause amino acids to appear more solvent accessible than they really are. Previous work suggested that hydrogen peroxide was the major secondary oxidant of concern in hydroxyl radical footprinting experiments; however, even after elimination of all hydrogen peroxide, some secondary oxidation was still detected. Evidence is presented for the formation of peptidyl hydroperoxides as the most abundant product upon oxidation of aliphatic amino acids. Both reverse phase liquid chromatography and catalase treatment were shown to be ineffective at eliminating peptidyl hydroperoxides. The ability of these peptidyl hydroperoxides to directly oxidize methionine is demonstrated, suggesting the value of methionine amide as an in situ protectant. Hydroxyl radical footprinting protocols require the use of an organic sulfide or similar peroxide scavenger in addition to removal of hydrogen peroxide to successfully eradicate all secondary oxidizing species and prevent uncontrolled oxidation of sulfur-containing residues.     

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.     

水溶性羧酸咔咯铁(Ⅲ)配合物对DNA的氧化断裂作用

合成了5,10,15-三(4-羧基-苯基)咔咯铁配合物(Fe^ⅢTCPC), 采用紫外-可见光谱、 荧光光谱、 圆二色光谱和黏度法研究了Fe^ⅢTCPC与小牛胸腺DNA(ct-DNA)的相互作用, 并用琼脂糖凝胶电泳研究了氧化剂参与下Fe^ⅢTCPC对pBR22 DNA的氧化断裂能力. 结果表明, Fe^ⅢTCPC与DNA的作用方式为外部结合模式, 其结合常数K_b=1.96×10⁵ L/mol. 在过氧化氢(H₂O₂)或叔丁基过氧化氢(TBHP)为氧化剂条件下, Fe^ⅢTCPC展现出良好的DNA氧化断裂能力, 且TBHP的氧化断裂效率比H₂O₂好. 用H₂O₂和TBHP为氧化剂时, Fe^ⅢTCPC可能是通过活性Fe^Ⅴ-oxo机制对DNA氧化断裂.     

Use of the hydroxyl radical and gel electrophoresis to study DNA structure

The hydroxyl radical has been used as a chemical probe to study in solution the structure of DNA and DNA-protein complexes. The hydroxyl radical abstracts a deoxyribose hydrogen atom, cleaving one strand of the DNA. The cutting pattern, visualized by separating the cleavage products using gel electrophoresis, shows the reactivity of each backbone position toward the radical. This method has been applied to studies of DNA bending and helical twist. Phased runs of adenines (adenine tracts) cause sequence-directed DNA bending. The hydroxyl radical cleavage of a bent DNA fragment containing short adenine tracts phased with the helix screw gives rise to an unusual cutting pattern. The hydroxyl radical cleavage rate decreases in the 5' to 3' direction along each adenine tract, with a minimum at the 3' end of each adenine tract. The cleavage of the matching thymine tract is similar, but the minimum in the pattern is offset in the 3' direction. This pattern on the autoradiograph of the gel is interpreted to indicate that bending is accompanied by a narrow minor groove in the DNA molecule. Furthermore, hydroxyl radical cleavage results in different cutting patterns for two similar sequences, (CGA4T4)5 and (CGT4A4)5, which have been shown to be bent and relatively straight, respectively. The hydroxyl radical method has also been used to determine the helical repeat of the metallothionein IIA gene to be about 10.5 base pairs per turn. Methods of optimizing the hydroxyl radical reaction for DNA-protein footprinting are discussed. Because individual gel bands give information about cutting frequency at particular positions in the backbone, gel resolution and clear autoradiographs are important to this work.(ABSTRACT TRUNCATED AT 250 WORDS)     

Photocleavage of lysozyme by cobalt(III) complexes

Photochemical reagents that cleave proteins at specific sites (photoproteases) are useful for studying protein structure and protein-ligand interactions. PolyammineCo(III) complexes are tested here as photochemical probes to cleave proteins. Irradiation of a mixture of lysozyme, a model protein, and polyammineCo(III) complexes resulted in the facile cleavage of the peptide backbone. Photocleavage yielded two fragments of molecular weights 10.6 and 3.7 kDa, and these masses sum to the molecular mass of lysozyme (14.3 kDa). No cleavage was detected in the absence of the metal complex, in the dark, or upon irradiation at wavelengths of >420 nm. The photocleavage yield increased with irradiation time and with the concentrations of the metal complex and the protein. N-terminal sequencing of the 10.6 kDa fragment indicated residues that are identical to the N-terminus of lysozyme, and sequencing of the 3.7 kDa fragment indicated Val-Ala-Trp-Arg, an internal sequence of lysozyme. From the known primary sequence of lysozyme and the sequencing data, the cleavage site was assigned to Trp108-Val109. Molecular modeling indicates that the observed cleavage site is within few angstroms from the proposed metal binding site at Glu35-Asp52. This is the first report of the successful photocleavage of proteins, with high selectivity, by transition metal complexes. This novel observation can facilitate the rational design of transition metal complexes for the photochemical footprinting of metal binding sites on proteins.     

A Hydroxyl-bridged Dinuclear Copper Complex Having Planar Structure Shows Efficient DNA Cleavage Activity in Aqueous Solution

A new dinuclear copper(II) complex, [Cu(DPA)OH]₂?2ClO₄(Cu₂-DPA₂, DPA = di(pyridin-2-yl)amine), was synthesized and structurally characterized. The complex crystallized in a triclinic P-1 space group, taking on a slightly distorted tetragonal geometry. Both Cu(II) in Cu₂-DPA₂ are bridged by two hydroxyl groups with a distance of 2.938 Å. The whole molecule is nearly co-planar with the exception of the bridging hydroxyl groups. Complex Cu₂-DPA₂ can cleave efficiently supercoiled pBR322 DNA into its nicked and linearized forms at micromolar concentrations in the presence of ascorbate near physiological conditions. The presence of standard radical scavengers does not have any apparent effect on the cleavage efficiency, suggesting that Cu(II) bound oxygen intermediates rather than freely diffusible hydroxyl radicals may act as the active species in the DNA scission. Comparison of the cleavage reactivity of Cu₂-DPA₂ with that of mononuclear analogue Cu-DPA and trinuclear Cu₃-L demonstrates that the synergistic effect between Cu(II) centers in Cu₂-DPA₂ is crucial for the DNA cleavage.     

丝组二肽所含基团在其切割DNA反应中的作用

近 2 0年来 ,人工核酸切割试剂的研究一直是化学、生物化学和分子生物学中最为活跃的前沿领域之一[1,2 ] .人工核酸切割试剂可以在足迹技术和核酸高级结构的研究中用作高分辨率的化学探针 ,还可以用于合成定点切割试剂[3] .后者又被称为人工工具酶 ,是一种非常重要的分子生物学工具 ,在疾病的基因治疗、反义 PCR技术等领域中都具有重要的应用 .人工核酸切割试剂的切割机理主要有自由基机理和磷酸酯水解机理两大类 .相对于自由基机理 ,水解机理具有许多优点 ,使得水解型切割试剂具有更为广泛的应用 .对于 DNA,目前文献报道的水解型人工切…     

Exploring both sequence detection and restriction endonuclease cleavage kinetics by recognition site via single-molecule microfluidic trapping

We demonstrate the feasibility of a single-molecule microfluidic approach to both sequence detection and obtaining kinetic information for restriction endonucleases on dsDNA. In this method, a microfluidic stagnation point flow is designed to trap, hold, and linearize double-stranded (ds) genomic DNA to which a restriction endonuclease has been pre-bound sequence-specifically. By introducing the cofactor magnesium, we determine the binding location of the enzyme by the cleavage process of dsDNA as in optical restriction mapping, however here the DNA need not be immobilized on a surface. We note that no special labeling of the enzyme is required, which makes it simpler than our previous scheme using stagnation point flows for sequence detection. Our accuracy in determining the location of the recognition site is comparable to or better than other single molecule techniques due to the fidelity with which we can control the linearization of the DNA molecules. In addition, since the cleavage process can be followed in real time, information about the cleavage kinetics, and subtle differences in binding and cleavage frequencies among the recognition sites, may also be obtained. Data for the five recognition sites for the type II restriction endonuclease EcoRI on λ-DNA are presented as a model system. While the roles of the varying fluid velocity and tension along the chain backbone on the measured kinetics remain to be determined, we believe this new method holds promise for a broad range of studies of DNA-protein interactions, including the kinetics of other DNA cleavage processes, the dissociation of a restriction enzyme from the cleaved substrate, and other macromolecular cleavage processes.     

Two new ternary complexes of copper(II) with tetracycline or doxycycline and 1,10-phenanthroline and their potential as antitumoral: cytotoxicity and DNA cleavage

This paper reports on the synthesis and characterization of two new ternary copper(II) complexes: [Cu(doxycycline)(1,10-phenanthroline)(H(2)O)(ClO(4))](ClO(4)) (1) and [Cu(tetracycline)(1,10-phenanthroline)(H(2)O)(ClO(4))](ClO(4)) (2). These compounds exhibit a distorted tetragonal geometry around copper, which is coordinated to two bidentate ligands, 1,10-phenanthroline and tetracycline or doxycyline, a water molecule, and a perchlorate ion weakly bonded in the axial positions. In both compounds, copper(II) binds to tetracyclines via the oxygen of the hydroxyl group and oxygen of the amide group at ring A and to 1,10-phenanthroline via its two heterocyclic nitrogens. We have evaluated the binding of the new complexes to DNA, their capacity to cleave it, their cytotoxic activity, and uptake in tumoral cells. The complexes bind to DNA preferentially by the major groove, and then cleave its strands by an oxidative mechanism involving the generation of ROS. The cleavage of DNA was inhibited by radical inhibitors and/or trappers such as superoxide dismutase, DMSO, and the copper(I) chelator bathocuproine. The enzyme T4 DNA ligase was not able to relegate the products of DNA cleavage, which indicates that the cleavage does not occur via a hydrolytic mechanism. Both complexes present an expressive plasmid DNA cleavage activity generating single- and double-strand breaks, under mild reaction conditions, and even in the absence of any additional oxidant or reducing agent. In the same experimental conditions, [Cu(phen)(2)](2+) is approximately 100-fold less active than our complexes. These complexes are among the most potent DNA cleavage agents reported so far. Both complexes inhibit the growth of K562 cells with the IC(50) values of 1.93 and 2.59 μmol L(-1) for compounds 1 and 2, respectively. The complexes are more active than the free ligands, and their cytotoxic activity correlates with intracellular copper concentration and the number of Cu-DNA adducts formed inside cells.     

化学核酸酶及其作用机理

化学核酸酶是一类人工设计、合成的DNA 或RNA 定位断裂工具, 由核酸识别结合系统和化学断裂系统组成。它们能够在任何位点断裂单链、双链DNA 或RNA , 不受限制性内切酶的天然专一性限制。本文除介绍了一些新的化学核酸酶体系外, 着重对它们的作用方式及作用机理进行了讨论。     

金属卟啉核酸定位断裂剂的设计及氧化断裂研究

金属卟啉连接到一些特殊基团如寡聚核苷酸、蛋白肽链、吖啶等上时, 可达到对DNA 的定位断裂, 这在核酸探针及抗癌剂的设计中具有重要的作用。本文就近年来国内外在金属卟啉对DNA 的定位识别及在Ph IO、KHSO 5、O 2? 还原剂等存在下, 对DNA 定位氧化断裂等方面的研究进展进行了综述, 可供该方向的研究人员参考。     

金属配合物-寡聚核苷酸定位断裂剂研究进展

核酸切割试剂与寡聚核苷酸(ODN)偶联制得的人工核酸酶能在特定位点断裂DNA或RNA,为人工核酸酶的分子设计提供了一种新方法.本文综述了金属配合物-ODN识别切割试剂的偶联方式及其与靶分子的作用机制,并指出了今后的研究方向.     

三元TBZ/HPB-铜(Ⅱ)-L-蛋氨酸配合物的合成、表征、抑菌活性及与DNA的作用

本文合成了2个新的三元铜(Ⅱ)配合物:[Cu(TBZ)(L-Met)(H2O)]ClO4.H2O(1)和[Cu(HPB)(L-Met)]ClO4(2)[TBZ=2-(4′-噻唑基)苯并咪唑,HPB=2-(2-吡啶)苯并咪唑,L-Met=L-蛋氨酸]。通过元素分析、摩尔电导率、IR、UV-Vis及电喷雾质谱对这些配合物进行了表征。用二倍稀释法研究了配合物的抗菌活性,发现配合物对金黄色葡萄球菌(Staphylococcus aureus,G+),枯草杆菌(Bacillussubtilis,G+),沙门氏杆菌(Salmonella,G-)和大肠杆菌(Escherichia coil,G-)具有良好的抑制作用。采用电子吸收光谱、荧光光谱、粘度测定及琼脂凝胶电泳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DNA作用,在维生素C存在下通过羟自由基.OH,单线态氧1O2或者1O2类似物如Cu-O2,切割pBR322 DNA双螺旋结构。     

基于镱和铒的α-噻吩甲酰丙酮-哌啶配合物与DNA之间相互作用的DNA探针和切割研究

两种[Ln(TTA)4].HP (Ln =Yb, Er)配合物被合成并表征。通过紫外可见光谱、荧光光谱、粘度和分子模拟研究了他们与DNA的键合特征。研究结果表明：它们能插入双链的DNA。更重要的是它们的荧光强度能被DNA增强,因此,一种灵敏的荧光检测DNA的方法被发展。两种配合物与质粒DNA的切割反应在凝胶电泳上展开。有意义的是,我们发现在pH=7.2 和 37℃下,两种化合物都能切割超螺旋质粒DNA。另外,我们选择BDNPP作为模型化合物进一步研究了它们对质粒DNA的切割机理,从一级动力学方程,我们间接证明可能是水解切割机理。     

Novel Water-Soluble 4,4-Disubstituted Ruthenium(III)-Salen Complexes in DNA Stranded Scission

Salen-type Ru(III) complexes are found to be capable of reacting with physiologically acceptable oxidants. The water solubility and DNA affinity of these Ru(III)-salen complexes are enhanced by the utilization of a variety of charged groups through the formation of peptide bonds. In the presence of hydrogen peroxide, modified Ru(III)-salen complexes are capable of nicking DNA. In addition, the reactivity in DNA cleavage increases along with the total number of positive charges retaining in Ru(III)-salen complexes and less influence in the electronic effect. Using ³²P-end-labeled oligonucleotides and high resolution polyacrylamide gel electrophoresis, Ru(III)-salen complexes are found to randomly cleave DNA regardless of the DNA secondary conformation such as bulge, inter-loop, or double-stranded regions. The possible reactive species of Ru(III)-salen complexes in DNA cleavage is considered as the hydroxyl radical and high valent oxoruthenium(IV) species according to the UV titration, quenching studies, and reaction with varied oxidants.     

A microfluidic SELEX prototype

Aptamers are nucleic acid binding species capable of recognizing a wide variety of targets ranging from small organic molecules to supramolecular structures, including organisms. They are isolated from combinatorial libraries of synthetic nucleic acid by an iterative process referred to as SELEX (Systematic Evolution of Ligands by Exponential Enrichment). Here we describe an automated microfluidic, microline-based assembly that uses LabView-controlled actuatable valves and a PCR machine, and which is capable of the selection and synthesis of an anti-lysozyme aptamer as verified by sequence analysis. The microfluidic prototype described is 1) a simple apparatus that is relatively inexpensive to assemble, making automated aptamer selection accessible to many investigators, and 2) useful for the continued “morphing” of macro→meso→microfabricated structures until a convergence to a few functional systems evolves and emerges, partly or completely achieving simpler, smaller and more rapid SELEX applications.     

Immobilization of DNAzyme catalytic beacons on PMMA for Pb2+ detection

Due to the numerous toxicological effects of lead, its presence in the environment needs to be effectively monitored. Incorporating a biosensing element within a microfluidic platform enables rapid and reliable determinations of lead at trace levels. A microchip-based lead sensor is described here that employs a lead-specific DNAzyme (also called catalytic DNA or deoxyribozyme) as a recognition element that cleaves its complementary substrate DNA strand only in the presence of cationic lead (Pb(2+)). Fluorescent tags on the DNAzyme translate the cleavage events to measurable, optical signals proportional to Pb(2+) concentration. The DNAzyme responds sensitively and selectively to Pb(2+), and immobilizing DNAzyme in the sensor permits both sensor regeneration and localization of the detection zone. Here, the DNAzyme has been immobilized on a PMMA surface using the highly specific biotin-streptavidin interaction. The strategy includes using streptavidin physisorbed on a PMMA surface to immobilize DNAzyme both on planar PMMA and on the walls of a PMMA microfluidic device. The immobilized DNAzyme retains its Pb(2+) detection activity in the microfluidic device and can be regenerated and reused. The DNAzyme shows no response to other common metal cations and the presence of these contaminants does not interfere with the lead-induced fluorescence signal. While prior work has shown lead-specific catalytic DNA can be used in its solubilized form and while attached to gold substrates to quantitate Pb(2+) in solution, this is the first use of the DNAzyme immobilized within a microfluidic platform for real time Pb(2+) detection.