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)     

Ferrocene‐bridging dinuclear cyclen copper(II) complexes as high efficient artificial nucleases: design,synthesis and interaction with DNA

Two novel cyclen copper(II) complexes bridged by ferrocene were designed and synthesized. Both of these complexes exhibited excellent cleavage ability towards plasmid DNA via an oxidative pathway without the presence of any additives. Cyclic voltammetry was used to investigate the electrochemistry characters of the interaction between the complexes and DNA. Agarose gel electrophoresis was carried out to study the DNA restriction ability of these complexes, and the results indicated that the complexes showed higher cleavage efficiency via an oxidative pathway without the presence of any additives. The mechanism of DNA cleavage catalyzed by these complexes was examined by the addition of various scavengers, and the results showed that singlet oxygen and hydroxyl radical might be responsible for the cleavage process. Copyright © 2008 John Wiley & Sons, Ltd.     

(E)-2-乙氧基乙基-2-氰基-3-((4-(2,4-二氟苯氧基)苄基)氨基)-3-甲氧基丙烯酸酯对超螺旋质粒DNA的特异性切割(英文）

研究了一种新型丙烯酸酯 (E)-2-乙氧基乙基-2-氰基-3-((4-(2,4-二氟苯氧基)苄基)氨基)-3-甲氧基丙烯酸酯(MAZ)对超螺旋pUC19 DNA的定点切割作用。利用紫外吸收、荧光光谱、凝胶电泳和DNA测序技术研究其核酸切割特异性。紫外吸收光谱的红移和减色效应,以及静态荧光淬灭表明MAZ与DNA的作用属于典型的插入模式。不仅如此,凝胶电泳条带的变化以及DNA测序结果表明DNA的定点切割是通过DNA双链的分步水解完成。     

Hydroxyl radical is the active species in photochemical DNA strand scission by bis(peroxo)vanadium(V) phenanthroline

Bis(peroxo)vanadium(V) complexes are widely investigated as anticancer agents. They exert their antitumor and cyctotoxic effects through inhibition of tyrosine phosphatases and DNA cleavage, respectively. The latter process remains poorly understood. The mechanism of DNA cleavage by NH(4)[(phen)V(O)(eta(2)-O(2))(2)] (phen = 1,10-phenanthroline) was investigated. Kinetic studies on DNA cleavage revealed that the complex is a single-strand nicking agent with no specificity. EPR experiments using 2,2,6,6-tetramethyl-4-piperidone (TMP) and 5,5'-dimethyl-1-pyrroline-N-oxide (DMPO) as spin-traps for singlet oxygen and hydroxyl radical, respectively, implicated hydroxyl radical production upon photodecomposition of bis(peroxo)vanadium(V). This was corroborated by benzoate inhibition of DNA strand scission and stoichiometric oxidation of 2-propanol to acetone upon irradiation of bis(peroxo)vanadium(V) phenanthroline. High-resolution polyacrylamide gel analysis of the vanadium cleavage reaction and [Fe(II)EDTA](2)(-)/H(2)O(2) resulted in comigration of "ladder" pattern bands, which superimposed when both reactions were run on the same lane. These findings identify hydroxyl radical produced from the photooxidation of the peroxo ligand on vanadium as the active species in DNA cleavage.     

Factors influencing the DNA nuclease activity of iron, cobalt, nickel, and copper chelates

A library of complexes that included iron, cobalt, nickel, and copper chelates of cyclam, cyclen, DOTA, DTPA, EDTA, tripeptide GGH, tetrapeptide KGHK, NTA, and TACN was evaluated for DNA nuclease activity, ascorbate consumption, superoxide and hydroxyl radical generation, and reduction potential under physiologically relevant conditions. Plasmid DNA cleavage rates demonstrated by combinations of each complex and biological co-reactants were quantified by gel electrophoresis, yielding second-order rate constants for DNA(supercoiled) to DNA(nicked) conversion up to 2.5 × 10(6) M(-1) min(-1), and for DNA(nicked) to DNA(linear) up to 7 × 10(5) M(-1) min(-1). Relative rates of radical generation and characterization of radical species were determined by reaction with the fluorescent radical probes TEMPO-9-AC and rhodamine B. Ascorbate turnover rate constants ranging from 3 × 10(-4) to 0.13 min(-1) were determined, although many complexes demonstrated no measurable activity. Inhibition and Freifelder-Trumbo analysis of DNA cleavage supported concerted cleavage of dsDNA by a metal-associated reactive oxygen species (ROS) in the case of Cu(2+)(aq), Cu-KGHK, Co-KGHK, and Cu-NTA and stepwise cleavage for Fe(2+)(aq), Cu-cyclam, Cu-cyclen, Co-cyclen, Cu-EDTA, Ni-EDTA, Co-EDTA, Cu-GGH, and Co-NTA. Reduction potentials varied over the range from -362 to +1111 mV versus NHE, and complexes demonstrated optimal catalytic activity in the range of the physiological redox co-reactants ascorbate and peroxide (-66 to +380 mV).     

Recent developments in DNA sequencing by capillary and microdevice electrophoresis

The present review covers papers published in the years 1997 and 1998 on DNA sequencing by capillary and microdevice electrophoresis. The article does not include other electrophoretic DNA applications such as analysis of oligonucleotides, genotyping, and mutational analysis. Capillary gel electrophoresis (CGE) is starting to become a viable competitor to slab gel electrophoresis for DNA sequencing. Commercially available multicapillary array sequencers are now entering sequencing facilities which to date have totally relied on traditional slab gel technology. CGE research on DNA sequencing therefore becomes increasingly concerned with the critical task of fine-tuning the operational parameters to create robust sequencing systems. Electrophoretic microdevices are being considered the next technological step in DNA sequencing by electrophoresis.     

Modulation of photo-oxidative DNA damage by cationic surfactant complexation

The natural packaging of DNA in the cell by histones provides a particular environment affecting its sensitivity to oxidative damage. In this work, we used the complexation of DNA by cationic surfactants to modulate the conformation, the dynamics, and the environment of the double helix. Photo-oxidative damage initiated by benzophenone as the photosensitizer on a plasmid DNA complexed by dodecyltrimethylammonium chloride (DTAC), tetradecyltrimethylammonium chloride (TTAC), cetyltrimethyammonium chloride (CTAC) and bromide (CTAB) was detected by agarose gel electrophoresis. By fluorescent titration in the presence of ethidium bromide (EB) and agarose gel electrophoresis, we experimentally confirmed the complexation diagrams with a critical aggregation concentration on DNA matrix (CAC DNA) delimiting two regions of complexation, according to the DNA-phosphate concentration. The study of the photo-oxidative damage shows, for the first time, a direct correlation between the DNA complexation by these surfactants and the efficiency of DNA cleavage, with a maximum corresponding to the CAC DNA for DTAC and CTAC, and to DNA neutralization for CTAC and CTAB. The localization of a photosensitizer having low water solubility, such as benzophenone, inside the hydrophobic domains formed by the surfactant aggregated on DNA, locally increases the photoinduced cleavage by the free radical oxygen species generated. The inefficiency of a water-soluble quencher of hydroxyl radicals, such as mannitol, confirmed this phenomenon. The detection of photo-oxidative damage constitutes a new tool for investigating DNA complexation by cationic surfactants. Moreover, highlighting the drastically increased sensitivity of a complexed DNA to photo-oxidative damage is of crucial importance for the biological use of surfactants as nonviral gene delivery systems.     

人的基因组及DNA序列分析──过去、现去及将来（上）

人的基因组研究已成为生命科学前沿领域中最热门的课题之一。ＤＮＡ序列分析是基因组研究的关键技术．本文对人的基因组分析及其对ＤＮＡ序列分析的要求进行了论述．对ＤＮＡ序列分析方法如板凝胶电泳自放射显影法、板凝胶电泳激光荧光法、毛细管电泳激光荧光法、阵列毛细管凝胶电泳激光荧光法。超薄层板在胶电泳激光荧光法作了详细评论．并对正在开发的不用凝胶电泳分离的直接测序新技术和新方法，如质谱法、原子探针法（扫描隧道显微镜、原子力显微镜）、杂交法、流动单分子荧光检测法等进行了评论。     

氮杂大环铈(Ⅲ)配合物与pUC19 DNA的相互作用

以一种1,4,7,10,13,16,19,22,25,28,31-十一氮杂2,5,8,11,14,17,20,23,26,29,32-十一酰基-环三十三烷的衍生物（CYC）为配体,在溶液中和Ce（Ⅲ,M）离子形成氮杂大环铈配合物（M-CYC）作为仿生催化剂,通过紫外光谱法、荧光光谱法和凝胶电泳法研究了M-CYC配合物与DNA的相互作用. 结果表明,M-CYC与小牛胸腺DNA（CT DNA）以嵌插方式相互作用,在pH = 8.16的缓冲体系中,其结合常数K_b = 2.0×10⁴ L/mol. 凝胶电泳结果表明,当自由基捕捉剂存在时,M-CYC可将超螺旋pUC19 DNA切割为缺刻型DNA,其切割方式为水解切割.     

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.     

Synthesis,DNA binding,and antimicrobial studies of novel metal complexes containing a pyrazolone derivative Schiff base

A novel series of Co(II), Ni(II), Cu(II), Zn(II), and VO(IV) complexes has been synthesized from the Schiff base derived from 4-[(3,4-dimethoxybenzylidene)amino]-1,5-dimethyl-2-phenyl-1,2-dihydropyrazol-3-one and 1,2-diaminobenzene. Structural features were determined by analytical and spectral techniques. Binding of synthesized complexes with calf thymus DNA (CT DNA) was studied by spectroscopic methods and viscosity measurements. Experimental results indicate that the complexes are able to form adducts with DNA and to distort the double helix by changing the base stacking. Lower DNA affinity of the VO(IV) complex is caused by the change of coordination geometry by the vanadyl ion resulting in a somewhat unfavorable configuration for the DNA binding. Oxidative DNA cleavage activities of the complexes were studied with supercoiled (SC) pUC19 DNA using gel electrophoresis; the mechanism studies revealed that the hydroxyl radical is likely to be the reactive species responsible for the cleavage of pUC19 DNA by the synthesized complexes. The in vitro antimicrobial screening effects of the investigated compounds were monitored by the disc diffusion method. The synthesized Schiff base complexes exhibit higher antimicrobial activity than the respective free Schiff base.     

Synthesis,characterization, DNA binding,oxidative damage of DNA strand scission,and antimicrobial activities of β-diketone condensed Schiff-base transition metal complexes

Co(II), Ni(II), Cu(II), Zn(II), and VO(IV) complexes containing a versatile β-diketone Schiff-base ligand (obtained by the condensation of 3-furan-2-ylmethylene-2,4-dione and 2-aminophenol) have been synthesized and characterized. Microanalytical, magnetic, and spectroscopic data reveal that the central metal is coordinated to two oxygens of phenolate and two nitrogens of imine of the ligand. Binding of synthesized complexes with calf thymus DNA has been investigated by spectroscopic and electrochemical methods and viscosity measurements. The complexes are able to form adducts with DNA and to distort the double helix by changing the base stacking. Electrostatic binding of vanadyl complex is observed from the weak hypochromism in electronic absorption spectra and no change in the viscosity with DNA. Oxidative DNA cleavage activities of the complexes are studied with supercoiled pUC19 DNA using gel electrophoresis. The hydroxyl radical (OH^?) is likely to be the species responsible for the cleavage of pUC19 DNA by the synthesized complexes. Under our experimental conditions, the vanadyl complex has no significant cleavage of DNA. The compounds have been screened for activity against several bacterial and fungal strains and the results are compared with the activity of standard drugs.     

A microfluidic device that generates hydroxyl radicals to probe the solvent accessible surface of nucleic acids

We describe a microfluidic device containing a mineral matrix capable of rapidly generating hydroxyl radicals that enables high-resolution structural studies of nucleic acids. Hydroxyl radicals cleave the solvent accessible backbone of DNA and RNA; the cleavage products can be detected with as fine as single nucleotide resolution. Protection from hydroxyl radical cleavage (footprinting) can identify sites of protein binding or the presence of tertiary structure. Here we report preparation of micron sized particles of iron sulfide (pyrite) and fabrication of a microfluidic prototype that together generate enough hydroxyl radicals within 20 ms to cleave DNA sufficiently for a footprinting analysis to be conducted. This prototype enables the development of high-throughput and/or rapid reaction devices with which to probe nucleic acid folding dynamics and ligand binding.     

Miniaturization of Slab Gel Electrophoresis Using Thermal Lens Microscope and its Application to Genetic Diagnostics

Slab gel electrophoresis is the most widely used separation method for DNA fragments, proteins and carbohydrates, and miniaturization of this process is expected to provide fast, inexpensive and convenient analyses. However, two problems concerning the miniaturization of gel electrophoresis have to be solved:the separation performance and spatial resolution of the detector. We demonstrated that the separation performance was improved by using a discontinuous gel in which a concentrating gel was used to stack the sample to a sharp band, and using thermal lens microscope (TLM), which is highly sensitive and has a spatial resolution of micron level even in light scattering matrices as a gel, such sharpened separated bands were successfully detected. In this paper, we developed a miniaturized slab gel electrophoresis apparatus, demonstrated high speed separation of DNA fragments, and applied it to genetic diagnosis of coronary heart disease.     

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。     

MECHANISM OF DNA CLEAVAGE MEDIATED BY PHOTOEXCITED NON-STEROIDAL ANTIINFLAMMATORY DRUGS

DNA damage photoinduced by four nonsteroidal antiinflammatory drugs (NSAID) have been investigated by neutral agarose gel electrophoresis. Upon irradiation at 300 nm, in phosphate buffered solution, benoxaprofen, naproxen, ketoprofen, tiaprofenic acid photosensitized the formation of single-strand breaks (SSB) in double stranded supercoiled phi X174 DNA. The efficiency of the cleavage is higher in argon saturated solutions than in aerated solutions and it is not correlated with the quantum yield of photodegradation of the drugs. Simultaneously with the DNA strand breaks, NSAID promote a weak reduction of the electrophoretic mobility of the supercoiled form that may be attributed to the formation of pyrimidine dimers or other DNA unwinding products. These photodimerization processes suggest the involvement of a triplet-triplet energy transfer between NSAID and DNA. Addition of mannitol and superoxide dismutase decreases the efficiency of the cleavage suggesting that HO. and O2.- are involved in the DNA cleavage. Unexpectedly, addition of sodium azide quenches the cleavage both in aerated or in deaerated solutions. Substituting H2O by D2O does not change the number of SSB thus suggesting that 1O2 does not take an important place in the cleavage of DNA. From our data we tentatively assume that the cleavage occurs through a radical mechanism that may involve in a first step an energy or an electron transfer. Gel sequencing on NSAID-photoinduced DNA breakage exhibits no particular specificity except in the case of benoxaprofen where a slight selectivity for cytosine is observed.     

A new trick (hydroxyl radical generation) for an old vitamin (B12)

Photolysis of hydroxocobalamin in the presence of plasmid DNA (pBR322) results in DNA cleavage. Temporal control of hydroxyl radical production and DNA strand scission by hydroxocobalamin was demonstrated using a 2-deoxyribose assay and a plasmid relaxation assay, respectively. The light-driven hydroxocobalamin-mediated catalytic formation of hydroxyl radicals was demonstrated using radical scavenging studies of DNA cleavage and via recycling of a hydroxocobalamin-resin conjugate several times without loss of efficacy.     

Flow-based and sieving matrix-free DNA differentiation by a miniaturized field flow fractionation device

DNA separation is typically done by gel electrophoresis based on its charge property. In our previous work, we reported that dielectrophoresis could be used to manipulate polystyrene nanoparticles' motion by using a miniaturized electrical field flow fractionation device (micro-EFFF) with a segmented electrode operated under a pulsed voltage (PV). In this work, we report the manipulation and separation of DNA molecules using the micro-EFFF. DNA motion was in situ visualized inside the device. Results revealed that dielectrophoresis governed DNA motion, which was strongly correlated with the pulse frequency but not the duty cycle of a PV. A longer retention time of DNA molecules was measured under a PV. The retention time increased with the length of DNA molecules. As the micro-EFFF is flow-based and sieving-matrix-free, it has a potential to be applied to sample preparation in a micrototal analysis system or when fractionated molecules are needed for downstream analysis.     

Imaging as a tool for improving length and accuracy of sequence analysis in automated fluorescence-based DNA sequencing

A new method of signal analysis for automated fluorescence-based DNA sequencing is presented. Signal resolution is a limiting factor in obtaining accurate sequence information beyond 400-450 nucleotides per gel lane. We have developed a computer program for the imaging of DNA bands in sequencing gels. The image analysis shows that distortions in the shapes of the bands decrease resolution of peaks observed served in the standard data plots. Reconstruction of the undistorted band shape prior to signal analysis substantially improves the resolution of peaks and may improve the accuracy and length of the contiguous sequence read. Image analysis identified other factors limiting the accuracy and length of automated DNA sequence analysis and provided a tool for evaluating various remedies. Our techniques should also be applicable in other systems, for example, in gel electrophoresis of proteins and DNA restriction fragments, and in scranning densitometry.     

PVP两亲性嵌段共聚物对超螺旋DNA的裂解活性

以PVP-Cl为大分子引发剂,经ATRP聚合制备得到窄分子量分布、结构可控的含不同亲水/疏水比例的两亲性聚N-乙烯基吡咯烷酮-b-聚N-甲基丙烯酰基-N＇-Boc-色氨酸酰胺基硫脲嵌段共聚物（PVP-b-PTrpAMT-I,II,III）.1H NMR核磁共振、GPC-MALLS以及凝胶电泳对嵌段共聚物的结构进行了表征...