Single-molecule measurements of trapped and migrating circular DNA during electrophoresis in agarose gels

The effect of agarose gel concentration and field strength on the electrophoretic trapping of open (relaxed) circular DNA was investigated using microscopic measurements of individual molecules stained with a fluorescent dye. Three open circles with sizes of 52.5, 115, and 220 kbp were trapped by the electric field (6 V/cm) and found to be predominately fixed and stretched at a single point in the gel. The length of the stretched circles did not significantly change with agarose concentration of the gels (mass fractions of 0.0025, 0.01, and 0.02). The relaxation kinetics of the trapped circles was also measured in the gels. The relaxation of the large open circles was found to be a slow process, taking several seconds. The velocity and average length of the 52.5 kbp open circles and 48.5 kbp linear DNA were measured during electrophoresis in the agarose gels. The velocity increased when the agarose concentrations were lowered, but the average length of the open-circle DNA (during electrophoresis) did not significantly change with agarose gel concentrations. The circles move through the gels by cycles of stretching and relaxation during electrophoresis. Linear dichroism was also used to investigate the trapping and alignment of the 52.5 kbp open circles. The results in this study provide information that can be used to improve electrophoretic separations of circular DNA, an important form of genetic material and commonly used to clone DNA.     

DNA NICKING BY ULTRAVIOLET RADIATION IS ENHANCED IN THE PRESENCE OF IRON and OF OXYGEN

Double-stranded covalently closed circular supercoiled DNA (ccc DNA) from plasmid pUK 9 was irradiated in vitro at denned wavelengths in the UV region (290, 313 and 365 nm). The nicking was monitored by electrophoresis on agarose gels, ethidium staining and densitometric quantitation of supercoiled and relaxed moieties. At the explored wavelengths, the dose required for introducing one nick per million phosphodiester bonds diminishes with increased concentration of added ferric iron, whereas the effect of cupric iron is practically negligible. Adding metal chelators or bubbling argon prior to the irradiation results in a dramatic increase in the dose required for introducing one nick per million phosphodiester bonds. Taken together, these results seem to indicate that iron and oxygen play a role as cofactors in the UV-induced nicking of ccc DNA in vitro.     

PSORALENS CLEAVE pBR322 DNA UNDER ULTRAVIOLET RADIATION

Supercoiled (SC) pBR322 was used to probe the recent claim that 5-geranoxylpsoralen (5-GOP) did not photoreact with DNA. Contrary to expectations, 5-GOP was found to damage DNA in the presence of UV-A through two competing pathways: (a) single strand breaks, identified by the conversion of supercoiled into open circular and linear DNA, and (b) cross-linking, revealed by the fluence-dependent decrease in the extent of denaturation of the double stranded supercoiled DNA to single stranded circular DNA. In addition, a fluence-dependent modification reduced the ability of the restriction enzyme EcoR I to linearize the photosensitized DNA, and alkali-labile lesions were generated. Psoralen, 5-methoxypsoralen, and 8-methoxypsoralen, which are well-known to undergo cycloaddition to DNA, had a more pronounced effect on supercoiled DNA. Single strand breaks occurred more readily than with 5-GOP, and the surviving SC form remaining had reduced electrophoretic mobility in agarose gels. In all cases, the DNA damage was more prominent when oxygen was absent.     

A simple system for staining protein and nucleic acid electrophoresis gels

Researchers in molecular biology spend a significant amount of time tending to the staining and destaining of electrophoresis gels. Here we describe a simple system, costing approximately $100 and taking approximately 1 h to assemble, that automates standard nucleic acid and protein gel staining protocols. Staining is done in a tray or, with DNA gels, in the electrophoresis chamber itself following automatic detection of the voltage drop. Miniature pumps controlled by a microcontroller chip exchange the necessary solutions at programmed time intervals. We demonstrate efficient and highly reproducible ethidium bromide and methylene blue staining of DNA in agarose gels and Coomassie blue and silver staining of proteins in polyacrylamide gels.     

Modification of the electrokinetic properties of reversible electrophoresis gels for the separation and preparation of DNA

The effect of adding linear polymers to a novel reversible electrophoretic was measured. Reversible gels are formed using the polyanionic carbohydrate polymer, gellan gum. Gellan gum forms strong stable gels in the presence of divalent cations or diamines. The gels are reversible (return to solution) by changing the ionic environment or pH. Gellan gum is an anionic polymer, and the electrophoresis gels have considerable electroosmotic flow (EOF) toward the negative electrode. We measured the EOF in gellan gum electrophoresis gels as a function of gel concentration, buffer composition, and linear polymer additive. The linear polymers used in this study were polyethylene oxide and hydroxyethyl cellulose. Both polymers reduced EOF in the gels, in a manner dependent on molecular weight. Polymers with high molecular weight were more effective at reducing EOF. The addition of polymers increased the resolution of low molecular weight DNA. Native gellan gum resolved DNA from approx 50,000 to 1000 bp. Addition of the polymers resolved DNA down to approx 50 bp, in some instances. The influence of the polymers on circular plasmid DNA was also investigated. Addition of high molecular weight polyethylene oxide reduced the electrophoretic mobility of the nicked circular form compared to the supercoiled form.     

Hydrolytic cleavage of DNA by quercetin manganese(II) complexes

Quercetin manganese(II) complexes were investigated focusing on its DNA hydrolytic activity. The complexes successfully promote the cleavage of plasmid DNA, producing single and double DNA strand breaks. The amount of conversion of supercoiled form (SC) of plasmid DNA to the nicked circular form (NC) depends on the concentration of the complex as well as the duration of incubation of the complexes with DNA. The maximum rate of conversion of the supercoiled form to the nicked circular form at pH 7.2 in the presence of 100 μM of the complexes is found to be 1.32 × 10⁻⁴ s⁻¹. The hydrolytic cleavage of DNA by the complexes was supported by the evidence from free radical quenching, thiobarbituric acid-reactive substances (TBARS) assay and T4 ligase ligation.     

Effects of pulse strength and pulse duration on in vitro DNA electromobility

Interstitial transport of DNA is a rate-limiting step in electric field-mediated gene delivery in vivo. Interstitial transport of macromolecules, such as plasmid DNA, over a distance of several cell layers, is inefficient due to small diffusion coefficient and inadequate convection. Therefore, we explored electric field as a novel driving force for interstitial transport of plasmid DNA. In this study, agarose gels were used to mimic the interstitium in tissues as they had been well characterized and could be prepared reproducibly. We measured the electrophoretic movements of fluorescently labeled plasmid DNA in agarose gels with three different concentrations (1.0%, 2.0% and 3.0%) subjected to electric pulses at three different field strengths (100, 200 and 400 V/cm) and four different pulse durations (10, 50, 75, 99 ms). We observed that: (1) shorter pulses (10 ms) were not as efficient as longer pulses in facilitating plasmid transport through agarose gels; (2) plasmid electromobility reached a plateau at longer pulse durations; and (3) plasmid electromobility increased with applied electric energy, up to a threshold, in all three gels. These data suggested that both pulse strength and duration needed to be adequately high for efficient plasmid transport through extracellular matrix. We also found that electric field was better than concentration gradient of DNA as a driving force for interstitial transport of plasmid DNA.     

Defect passivation of CsPbI_2Br perovskites through Zn(Ⅱ) doping:toward efficient and stable solar cells

Defect passivation is an important strategy to achieve perovskite solar cells(PVSCs) with enhanced power conversion efficiencies(PCEs) and improved stability because the trap states induced by defects in the interfaces and grain boundaries of perovskites are harmful to both large open circuit voltage and high photocurrent of devices. Here, zinc cations(Zn~(2+)) were used as a dopant to passivate defects of the CsPbI_2Br perovskite leading to Zn~(2+)-doped CsPbI_2Br film with fewer trap states, improved charge transportation, and enhanced light-harvesting ability. Thus, the best-performance PVSC based on CsPbI2 Br with the optimal Zn~(2+)doping shows a higher PCE of 12.16% with a larger open-circuit voltage(V_(OC)) of 1.236 V, an improved shortcircuit current(J_(SC)) of 15.61 mA cm~(-2) in comparison with the control device based on the pure CsPbI_2Br which exhibits a PCE of 10.21% with a V_(OC)of 1.123 V, a J_(SC)of 13.27 mA cm~(-2). Time-resolved photoluminescence results show that the Zn~(2+)doping leads to perovskite film with extended photoluminescence lifetime which means a longer diffusion length and subsequently enhanced photocurrent and open circuit voltage. This work provides a simple strategy to boost the performance of PVSCs through Zn~(2+)doping.     

A microfluidic study of mechanisms in the electrophoresis of supercoiled DNA

In this work, microfluidic chips were used to study the electrophoresis of supercoiled DNA (SC DNA) in agarose. This system allowed us to study the electrophoretic and trapping behaviours of SC DNA of various lengths, at various fields and separation distances. Near a critical electric field the DNA is trapped such that the concentration falls exponentially with distance. The trapping of such circular DNA has been explained in terms of the 'lobster trap' or 'impalement' model where shorter fibres become trapping sites at higher fields, leading to an ongoing (and gradual) increase in trapping with increasing field. By contrast, the present study suggests that under some circumstances the traps have a barrier such that only when the DNA has sufficient energy (at high enough fields) can it become trapped, leading to a sudden transition in behaviours at the critical field. We propose an 'activated impalement' mechanism of trapping in which only at sufficiently high fields is the SC DNA impaled and trapped for long times. The critical electric field appears to be inversely proportional to the length of the DNA molecule, suggesting that the force required to impale the SC DNA is constant.     

Separation of different physical forms of plasmid DNA using a combination of low electric field strength and flow in porous media: effect of different field gradients and porosity of the media

The retention of different physical forms of DNA by an electric field in a chromatography system was studied. We were able to effectively separate the supercoiled and the open circular forms of plasmid DNA using this type of electrochromatography system. Chromatography columns were packed with porous beads, and an axial electric field was applied so that convective buffer flow opposed the direction of electrophoresis of the DNA. A model system composed of approximately equal amounts of the super-coiled and open circular forms of the plasmid pBR 322 (4322 base pairs) was used to test the separation. Chromatography beads (agarose-based) with different porosities were used to determine the effect of the stationary phase on the separation. The porous media did not have a major effect on the separation, but the best separations were obtained using porous chromatography media made with the highest agarose concentration (10% agarose). Selective elution of plasmid DNA with different forms was obtained by either increasing the flow rates or decreasing the electric field strength (by steps or a gradient). In all the separations, the more compact supercoiled form of the plasmid was retained less strongly than either the open circular form (nicked) or the linear form. High molecular weight host genomic DNA was more strongly retained than the plasmid DNA. Increasing the ionic strength of the buffer improved resolution and capacity. The capacity of the separation was determined by injecting increasing amounts of plasmid DNA. Satisfactory separation was obtained at sample loading of up to 360 microg of total DNA on a column with dimensions of 2.5 by 11 cm (bed volume of 54 mL). The retention of DNA depends upon a counter-current flow of electrophoresis and convective flow and could be regarded as a type of field flow fractionation. The retention of the DNA by the electric field and flow is discussed in relation to the diffusion coefficients of the DNA.     

DNA-hydrolyzing autoantibodies

Catalysis by antibodies could be a frequent phenomenon if the immune system generates a sufficiently diverse number of antibodyactive sites, some of which may possess catalytic activity. A catalytic antibody can be expected to do more damage than one that simply binds antigen. The best biochemical marker of systemic lupus erythematosus (SLE) is presence of autoantibodies to DNA. In the present article, we describe the DNA-hydrolyzing activity of DNA-binding autoantibodies purified from SLE patients. The substrates employed were supercoiled plasmid, radiolabeled plasmid fragments, and oligonucleotides. Hydrolysis of DNA by the antibodies was indicated by the appearance of fragments visualized by ethidium bromide staining of agarose gels or autoradiography of polyacrylamide gels. Changes in linear dichroism values were also indicative of DNA hydrolysis. The antibody activity was purified by protein A-sepharose chromatography, high-performance liquid chromatography gel filtration, and DNA-affinity chromatography. Scrupulous control studies were done to demonstrate that DNA-hydrolyzing activity really belongs to the antibodies. Purified Fab fragments showed hydrolyzing activity, whereas the Fc fragment was inactive. The specificity of DNA cleavage was investigated, and the rate parameters of hydrolysis by antibodies and conventional nucleases were compared.     

β-K4H3[SiW9O37(CpTi)3]·11H2O环戊二烯钛多酸衍生物与DNA作用研究

某些过渡金属配合物具有特异性催化DNA和RNA断裂的功能, 因而研究过渡金属配合物对DNA和RNA的断链反应对新型抗肿瘤、抗艾滋病化学药物的定向设计及其基因治疗和分子生物学中DNA和RNA的高度专一性定点断裂、 DNA定位诱变和构象识别具有重要意义和应用前景[1,2]. 我们对二茂钛多酸有机金属衍生物合成及抗肿瘤活性研究表明, 环戊二烯钛多氧金属酸盐衍生物具有很高的抗肿瘤活性和较好的水溶性及稳定性, 有潜在的抗肿瘤药用价值[3].     

硫杂蒽酮镍（II）配合物与DNA的作用研究

合成了O-（硫杂蒽酮-[2]-基）-氧乙酸镍（II）配合物。通过元素分析,IR, DTA-TG谱对其结构进行了表征。研究表明：配体羧羰基脱质子后与镍离子配位,配合物中含有一定量的配位水。同时以紫外可见光谱、荧光光谱、园二色谱,电化学方法和凝胶电泳方法研究了该配合物与DNA的作用。结果表明,该配合物能在生理条件下比配体和金属离子更有效地切割质粒DNA,自由基捕捉剂的加入不影响配合物的切割活性。该配合物使DNA溶液的紫外吸收强度和园二色吸收强度降低,DNA的存在可使该配合物的氧化还原活性降低。与溴化乙锭和DNA的竞争反应说明,该配合物主要以嵌入方式与DNA结合。     

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.     

Counterion-dye staining for DNA in electrophoresed gels using indoine blue and methyl orange

In this study, we describe a sensitive staining method for DNA in agarose and polyacrylamide gels using organic visible dyes, indoine blue (IB) and methyl orange (MO). The counterion-dye staining method uses two oppositely charged dyes to form a hydrophobic ion pair complex in the staining solution. A decrease in the number of free forms of dyes in staining solution can enhance the selectivity of binding between the dye and DNA, and can reduce nonspecific background staining. As a result, the sensitivity of counterion-dye staining was significantly improved compared with other dye-based staining. This method uses a staining solution consisting of 0.008% IB, 0.002% MO, 10% ethanol and 0.2 M sodium acetate at pH 4.7, and can detect 5 ng of lambda DNA/HindIII within 60 min in agarose gels and 10 ng of PhiX174 DNA/HaeIII within 20 min in polyacrylamide gels.     

Stabilization of thin-layer agarose gels after isoelectric focusing with polyacrylamide enables reverse imidazole-zinc staining and facilitates two-dimensional gel electrophoresis

Large-pore-size agarose gels provide excellent resolving capacity for high molecular weight biomolecules. Thin-layer agarose isoelectric focusing (IEF) gels on polyester support films are especially useful for the separation of large proteins based on their pI in native conformation, but the method has suffered from the lack of detection methods compatible with agarose gels in hydrated form. Recently, an acrylamide copolymerization method was reported to enable mass-spectrometry-compatible silver staining and in-gel digestion of proteins. In this study, the method was further applied by demonstrating successful reverse imidazole-zinc staining of thin-layer agarose IEF gels copolymerized with acrylamide. The sensitivity of the reverse staining method on the composite gel at its best equaled the sensitivity of the traditional dried agarose silver staining method. Owing to the increased durability and reversible detection, the reverse-stained first-dimension gel could be conveniently prepared for the second-dimension sodium dodecyl sulfate polyacrylamide gel electrophoresis by reduction and alkylation. In addition, the micropreparative generation of tryptic peptides of Coomassie brilliant blue R-250 stained proteins in the composite gel is demonstrated.     

The electric field dependence of DNA mobilities in agarose gels: a reinvestigation

The electric field dependence of the electrophoretic mobility of linear DNA fragments in agarose gels was reinvestigated in order to correct the observed mobilities for the different temperatures actually present in the gel during electrophoresis in different electric field gradients. When corrected to a common temperature, the electrophoretic mobilities of DNA fragments less than or equal to 1 kilobase pairs (kbp) in size were independent of electric field strength at all field strengths from 0.6 to 4.6 V/cm if the gels contained less than or equal to 1.4% agarose. The mobilities of larger DNA fragments increased approximately linearly with electric field strength. If the agarose concentration was higher than 2%, the mobilities of all DNA fragments increased with increasing electric field strength. The electric field dependence of the mobility was larger in gels cast and run in Tris-borate buffer (TBE) than in gels cast and run in Tris-acetate buffer (TAE), and was more pronounced in gels without ethidium bromide incorporated in the matrix. Ferguson plots were constructed for the various DNA fragments, both with and without extrapolating the temperature-corrected mobilities to zero electric field strength. Linear Ferguson plots were obtained for all fragments less than or equal to 12 kbp in size in agarose gels less than or equal to 1.4% in concentration if the mobilities were first extrapolated to zero electric field strength. Concave upward curvature of the Ferguson plots was observed for DNA fragments greater than or equal to 2 kbp in size at finite electric field strengths. Convex downward curvature of the Ferguson plots was observed for DNA fragments greater than or equal to 1 kbp in size in agarose gels greater than or equal to 2% in concentration. The mobilities of the various DNA fragments, extrapolated to zero agarose concentration and zero electric field strength, decreased with increasing DNA molecular weight; extrapolating to zero molecular weight gave an "intrinsic" DNA mobility of 2.7 x 10(-4) cm2/Vs at 20 degrees C. The pore sizes of LE agarose gels cast and run in TAE and TBE buffers were estimated from the mobility of the DNA fragments.(ABSTRACT TRUNCATED AT 400 WORDS)     

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.     

Ru(TAP)3]2+-photosensitized DNA cleavage studied by atomic force microscopy and gel electrophoresis: a comparative study

Topological modifications of plasmid DNA adsorbed on a variety of surfaces were investigated by using atomic force microscopy (AFM). On mica modified with 3-aminopropyltriethoxysilane (APS) or poly-L-lysine, the interaction between the plasmid DNA and the surface "freezes" the plasmid DNA conformation deposited from solution, and the AFM images resemble the projection of the three-dimensional conformation of the plasmid DNA in solution. Modified mica with low concentrations of Mg(2+) leads to a decrease in the interaction strength between plasmid DNA and the substrate, and the AFM images reflect the relaxed or equilibrium conformation of the adsorbed plasmid DNA. Under these optimized deposition conditions, topological modifications of plasmid DNA were produced under irradiation in the presence of [Ru(TAP)(3)](2+) (TAP = 1,4,5,8-tetraazaphenanthrene), which is a non-intercalating complex, and were followed as a function of illumination time. The observed structural changes correlate well with the conversion of the supercoiled covalently closed circular form (ccc form) into the open circular form (oc form), induced by a single-strand photocleavage. The AFM results obtained after fine-tuning of the plasmid DNA-substrate interaction compare well with those observed from gel electrophoresis, indicating that under the appropriate deposition conditions, AFM is a reliable technique to investigate irradiation-induced topological changes in plasmid DNA.