Separation-based approach to study dissociation kinetics of noncovalent DNA-multiple protein complexes

Noncovalent binding of DNA with multiple proteins is pivotal to many regulatory cellular processes. Due to the lack of experimental approaches, the kinetics of assembly and disassembly of DNA-multiple proteins complexes have never been studied. Here, we report on a first method capable of measuring disassembly kinetics of such complexes. The method is based on continuous spatial separation of different complexes. The kinetics of multiple complex dissociation processes are also spatially separated, which in turn facilitates finding their rate constants. Our separation-based approach was compared with a conventional no-separation approach by using computer simulation of dissociation kinetics. It proved to be much more accurate than the no-separation approach and to be a powerful tool for testing hypothetical mechanisms of the disassembly of DNA-multiple proteins complexes. An experimental implementation of the separation-based approach was finally demonstrated by using capillary electrophoresis as a separation method. The interaction between an 80 nucleotide long single-stranded DNA and single-stranded DNA binding protein was studied. DNA-protein complexes with one and two proteins were observed, and rate constants of their dissociation were determined. We foresee that a separation approach will be also developed to study the kinetics of the formation of DNA-multiple protein complexes.     

Folding and unfolding kinetics of DNA hairpins in flowing solution by multiparameter fluorescence correlation spectroscopy

Dynamic equilibrium between the folded and unfolded conformations of single stranded DNA hairpin molecules containing polythymine hairpin loops was investigated using simultaneous two-beam fluorescence cross-correlation spectroscopy and single beam autocorrelation spectroscopy. The hairpins were end-labeled with a fluorescent dye and a quencher, such that folding and unfolding of the DNA hairpin primary structure caused the dye fluorescence to fluctuate on the same characteristic time scale as the folding and unfolding reaction. These fluctuations were observed as the molecules flowed sequentially between two spatially offset, microscopic detection volumes. Cross-correlation analysis of fluorescence from the two detection volumes revealed the translational diffusion and flow properties of the hairpins, as well as the average molecular occupancy of the two volumes. Autocorrelation analysis of the fluorescence from the individual detection volumes revealed the kinetics of hairpin folding and unfolding, with the parameters relating to diffusion, flow, and molecular occupancy constrained to the values determined from the cross-correlation analysis. This allowed unambiguous characterization of the folding and unfolding kinetics, without the need to determine the hydrodynamic properties by analyzing a separate control sample. The analysis revealed nonexponential relaxation kinetics and DNA size-dependent folding times characteristic of dynamic heterogeneity in the DNA hairpin-forming mechanism.     

Extracting stoichiometry, thermodynamics, and kinetics for the interaction of DNA with cadmium ion by capillary electrophoresis on-line coupled with electrothermal atomic absorption spectrometry

Understanding the binding of cadmium with DNA is of great importance for elucidating the mechanism of cadmium genotoxicity and carcinogenicity. In the present work, CE on-line coupled with electrothermal atomic absorption spectrometry was employed to study the binding electrophoretic behaviors, stoichiometry, thermodynamics, and kinetics for the interaction of cadmium cation (Cd(II)) with DNA. The stoichiometry (Cd(II) to DNA (as the concentration of base pairs)) for the interaction was determined to be 1:5. Two types of binding sites on DNA were observed with the binding constants of 10(6) and 10(5) L/mol, respectively, showing strong affinity of Cd(II) to DNA. The interaction of Cd(II) with both types of binding sites on DNA were driven by negative enthalpy change with a large positive entropy change. The binding of Cd(II) to DNA followed a first-order kinetics for Cd(II) with the apparent activation energy of 45.7 +/- 1.9 kJ/mol. The results obtained in present investigation would be helpful to understanding the genotoxicity and carcinogenicity of cadmium.     

Effect of additives on swelling of covalent DNA gels

The volumetric response of polymer gels on cosolute addition depends on the interaction of the polymer with the cosolute and can be used as a simple and sensitive way of elucidating these interactions. Here we report on DNA networks, prepared by crosslinking double-stranded DNA with ethylene glycol diglycidyl ether (EGDE); these have been investigated with respect to their swelling in aqueous solution containing different additives, such as metal ions, polyamines, charged proteins, and surfactants. The deswelling on addition of metal ions occurs at lower concentrations with increasing valency of the counterion. The collapse of the gels in the presence of trivalent ions seems to follow the same kind of mechanism as the interaction in solution, but addition of these ions leads to DNA denaturation and formation of single-stranded DNA. Striking features were found in the deswelling of DNA gels by chitosan, spermine, spermidine, lysozyme, poly-l-lysine and poly-l-arginine. Chitosan is the most efficient cosolute of those investigated with respect to DNA gel collapse. The effect of the cationic surfactant tail length on the volume phase transition of DNA gels was studied as a function of surfactant concentration. Cationic surfactants effectively collapsed the gel from the critical aggregation concentration (cac), decreasing with increasing length of the hydrophobic tail. In several cases, the deswelling as a function of cosolute concentration shows a pronounced two-step behavior, which is interpreted in terms of a combination of DNA chain condensation and general osmotic deswelling. The studies included investigations on the state of the DNA chain after deswelling, on the reversibility of the deswelling as well as on the kinetics. With the exception for the trivalent lanthanide ions, it appears that the DNA chain always retains a double-helix conformation; with these metal ions, single-stranded DNA is found. The deswelling appears to be reversible as exemplified by addition of anionic surfactant subsequent to gel collapsed by cationic surfactant and addition of sodium bromide to gels collapsed by a polycation. An investigation of the kinetics shows that an increase in the surfactant tail length gives a pronouncedly slower deswelling kinetics.     

Drying of DNA droplets

The evaporation kinetics of droplets containing DNA was studied, as a function of DNA concentration. Drops containing very low DNA concentrations dried by maintaining a constant base, whereas those with high concentration dried with a constant contact angle. To understand this phenomenon, the distribution of the DNA inside the droplet was measured using confocal microscopy. The results indicated that the DNA was condensed mostly on the surface of the droplets. In the case of high concentration droplets, it formed a shell, whereas isolated islands were found for droplets of low DNA concentrations. Rheologic results indicate the formation of a hydro gel in the low concentration drops, whereas phase separation between the self-assembled DNA structures and the water phase occurred at higher concentration.     

Tritium/Protium Fractionation Near and Inside DNA

The fractionation factor of tritium between water and DNA as well as between water and the first hydration shell of DNA is determined. For this purpose the sublimation kinetics of water from DNA dissolved in water were determined at -200 °C and tritium was measured in the remaining water free DNA. The last sublimating water fractions showed a tritium level of about 1.4, the residual water free DNA about 1.9 units above the bulk water. The tritium accumulation inside and near DNA is attributed to the thermodynamic triton-proton exchange isotope effect existing between the strong hydrogen bridges of water and weaker hydrogen bridges as well as inside DNA as between the first hydration shell and DNA.     

Expanded Bed Chromatography as a Tool for Nanoparticulate Separation: Kinetic Study and Adsorption of Protein Nanoparticles

Expanded bed adsorption was investigated together with its suitability for the practical recovery of nanoparticulate mimics of products such as plasmid DNA and viruses as putative gene therapy vectors. The study assessed the binding of protein nanoparticles fabricated from bovine serum albumin (BSA) with average size of 80 nm as a model system and viral size/charge mimic to the streamline DEAE adsorbent in the expanded bed column chromatography. The adsorption kinetics and adsorption mechanism for the BSA nanoparticles on the adsorbent were studied. In batch adsorption studies, the factors nanoparticle concentration, contact time and adsorbent amount, affecting adsorption isotherms were investigated. Subsequently the data were regressed against the Lagergren equation, which represents a first-order kinetics equation and also against a pseudo-second-order kinetics equation. The results demonstrated that the adsorption process followed a Langmuir isotherm equation. The kinetics of the adsorption process followed a pseudo-second-order kinetics model with a rate constant value of 0.025 g mg^?1 min^?1. The dynamic binding capacity of the BSA nanoparticles on an expanded bed was calculated. The recovery of the nanoparticles was more than 85%.     

DNA recognition interfaces: the influence of interfacial design on the efficiency and kinetics of hybridization

The effect of the surface chemistry of DNA recognition interfaces on DNA hybridization at a gold surface was investigated using both electrochemistry and the quartz crystal microbalance (QCM) technique. Different DNA recognition interfaces were prepared using a two-component self-assembled monolayer consisting of thiolated 20-mer probe single-stranded DNA (ss-DNA) containing either a 3'-mercaptopropyl or a 3'-mercaptohexyl linker group and an alcohol-terminated diluent layer with 2-, 6-, or 11-carbon length. The influence of the interfacial design on the hybridization efficiency, the affinity constant (Ka) describing hybridization, and the kinetics of hybridization was assessed. It was found that the further the DNA was above the surface defined by the diluent layer the higher the hybridization efficiency and Ka. The kinetics of DNA hybridization was assessed using both a QCM and an electrochemical approach to ascertain the influence of the interface on both the initial binding of target DNA to the surface and the formation of a complete duplex. These measurements showed that the length of the diluent layer has a large impact on the time taken to form a perfect duplex but no impact on the initial recognition of the target DNA by the immobilized probe DNA.     

Influence of astaxanthin, zeaxanthin and lutein on DNA damage and repair in UVA-irradiated cells

In order to gain more knowledge about the antioxidant role of the predominant carotenoids (lutein and zeaxanthin) of the human retina, this study investigated their antioxidant activity and capacity. Astaxanthin was also studied, because its structure is very close to that of lutein and zeaxanthin. The antioxidant activity of these molecules was evaluated using chemiluminescence techniques, with lucigenin and luminol as chemiluminogenic probes for the superoxide radical and hydrogen peroxide, respectively. It was found that all three carotenoids have similar superoxide-scavenging activity. The effect on the reduction of H(2)O(2)-luminol chemiluminescence was present in the following order, zeaxanthin>astaxanthinlutein. Possible antioxidant capacity of these three compounds was sought using a biological system consisting of SK.N.SH human neuroblastoma and rat trachea epithelial cells subjected to oxidative stress from exposure to UVA radiation. In particular, we determined whether these compounds were capable of minimizing DNA damage and influencing the kinetics of DNA repair. DNA damage was assessed using the Comet assay, a rapid and sensitive single-cell gel electrophoresis technique used to detect primary DNA damage in individual cells. Neuroblastoma cells appeared more resistant to oxidative irradiation insult. The presence of carotenoids reduced DNA damage when rat epithelial cells were exposed to UVA radiation for 2min. A different result was obtained in experiments performed on neuroblastoma cells; in this case, the presence of carotenoid during UVA exposition increased the damage. The addition of carotenoids to epithelial cells after 2min of UVA exposition did not seem to improve the kinetics of DNA repair; on the contrary, zeaxanthin (after 60' incubation) and lutein (after 180' incubation) showed a genotoxic effect. The addition of carotenoids to neuroblastoma cells after 30' UVA exposition positively influences the kinetics of DNA repair in the first 15min of incubation. At longer exposition times, while the behaviour measured was not constant, a genotoxic effect was not observed. The data from this study provide additional information on the antioxidant and pro-oxidant activities of the predominant macular pigment carotenoids of the human retina.     

Enantioselective DNA threading dynamics by phenazine-linked.

The interactions between the stereoisomers of the chiral bis-intercalator [mu-C4(cpdppz)(2)-(phen)(4)Ru(2)](4+) and DNA reveal interesting dynamic discrimination properties. The two enantiomers Delta-Delta and Lambda-Lambda both form very strong complexes with calf thymus DNA with similar thermodynamic affinities. By contrast, they display considerable variations in their binding kinetics. The Delta-Delta enantiomer has higher affinity for calf thymus DNA than for [poly(dA-dT)](2), and the association kinetics of the dimer to DNA, as well as to polynucleotides, requires a multiexponential fitting function. The dissociation reaction, on the other hand, could be described by a single exponential for [poly(dA-dT)](2), whereas two exponentials were required for mixed-sequence DNA. To understand the key mechanistic steps of the reaction, the kinetics was studied at varied salt concentration for different choices of DNA and chirality of the threading complex. The enantiomers were found to have markedly different dissociation rates, the Lambda-Lambda enantiomer dissociating about an order of magnitude faster than the Delta-Delta enantiomer. Also, the salt dependence of the dissociation rate constants differed between the enantiomers, being stronger for the Lambda-Lambda enantiomer than for the Delta-Delta enantiomer. Since the dissociation reaction requires unthreading of bulky parts of the bis-intercalator through the DNA helix, a considerable conformational change of the DNA must be involved, possibly defining the rate-limiting step.     

ALKALI-LABILE LESION and URACIL-DNA-GLYCOSYLASE-SENSITIVE SITE REMOVAL AFTER BrdUrd and UVB TREATMENT OF CHINESE HAMSTER CELLS*

Abstract— A marked cell-cycle dependency for the recovery of cells after BrdUrd/UVB treatment has led us to look for similar characteristics in the molecular events associated with DNA repair. Such characteristics are reported here for the repair of alkali-labile lesions. When asynchronously growing cells were uniformly substituted with BrdUrd (a condition that results in the greatest cell killing), the repair kinetics followed a simple exponential response with a half-time of approximately 17min. However, when lesions were restricted to3–5% of the genome and the repair observed in the mid-S phase (a condition associated with sublethal damage repair), the DNA repair kinetics were complex. The rejoining of the DNA was biphasic with greater than 90% of the lesion with a half-time of less than6–7 min. Uracil removal followed similar kinetics. Caffeine, a potent inhibitor of cell survival after BrdUrd/UVB treatment, had no measurable effect on either uracil removal or alkali-labile lesion repair.     

Effects of DNA mismatches on binding affinity and kinetics of polymerase-DNA complexes as revealed by surface plasmon resonance biosensor

In this study, surface plasmon resonance (SPR) biosensor techniques were used to obtain quantitative information on the kinetics of the DNA and polymerase I (Klenow fragment) interaction. DNA duplexes containing different base compositions at the binding site were immobilized on the SPR sensor surface via biotin-streptavidin chemistry and the subsequent binding of the polymerase was measured in real time. Various kinetic models were tested and a translocation model was shown to provide the best fit for the binding and dissociation profiles. The results revealed that the enzyme binds to DNA at both the polymerase and the exonuclease domains with different association and dissociation rates as well as affinity constants, depending on the presence of mismatches near the primer 3'-end. Introduction of unpaired bases increases the DNA binding affinity towards the exonuclease domain and promotes the translocation of DNA from the polymerase site to the exonuclease site. The results also demonstrated that SPR biosensors may be used as a sensitive technique for studying molecular recognition events such as single-base discrimination involved in protein-DNA interaction.     

Study of electronic excitation energy transfer between cyanine dye molecules noncovalently bound to DNA

Electronic excitation energy transfer between molecules of carbocyanine dyes noncovalently bound to DNA was studied. 3,3′,9-Triethyl-5,5′-dimethyloxacarbocyanine iodide and 3,3′-dimethyl-9-ethyloxacarbocyanine iodide were used as energy donors, and 3,3′-diethylthiacarbocyanine iodide served as an acceptor dye. The fluorescence decay kinetics of the donors and its quenching by the acceptor in the presence of DNA were measured. The microphase model was used for interpretation of the experimental data, with allowance for concentrating dye molecules in the vicinity of DNA molecules.     

基于线性荧光探针对T4 DNA连接酶的活性分析

利用线性荧光探针作为核酸连接反应的模板和信号分子, 通过实时监测荧光信号的降低来表征连接产物的生成过程, 从而建立了一种连续、简单且特异性高的T4 DNA连接酶活性分析的新方法, 检出限可达1.2 U/mL; 同时, 该方法还可用于快速考察金属离子和化学药物对酶促反应的影响. 实验结果表明, 该法不仅为灵敏、实时监测核酸连接反应提供了一种简便快捷的非同位素分析方法, 也为开展核酸连接酶活性分析、反应动力学机制探讨和药物快速筛选提供了一种新技术.     

MEASUREMENT OF DNA CROSSLINKS BY S1 NUCLEASE: INDUCTION AND REPAIR IN PSORALEN-PLUS-360 nm LIGHT TREATED ESCHERICHIA COLI

Abstract—DNA crosslinks in Escherichia coli cells. exposed to 4.5',8-trimethylpsoralen plus 360 nm light, were measured using a rapid and sensitive new approach. The assay is based on the specificity of S₁ nuclease from Aspergillus oryzae to single-stranded DNA. Bacterial cells were lysed and the DNA denatured by alkali. Following acid neutralization. crosslinked DNA undergoes spontaneous renaturation and is rendered S₁-nuclease resistant and therefore acid-precipitable. The single-stranded fraction after denaturation by alkali decreases with increasing near UV light exposure in the presence of TMP following first order kinetics. The kinetics were faster when exposure was at 4°C rather than at 20°C. This suggests that excision of crosslinks occurs during exposure at the higher temperature. Indeed. since the rate of DNA crosslinking in a uvr B mutant which is excision-deficient was higher than in wild type bacteria at 4°C, some excision must have occurred even in the cold. DNA from excision-proficient cells incubated at 37°C following exposure to TMP-plus-near UV at 4° showed a greater single stranded fraction than that from non-incubated cells. This indicates repair of DNA crosslinks. which proceeded with a half-time of 8 min at 37°C and was unaffected by substitution of thymine in DNA by 5-bromouracil.     

Kinetics of comet formation in single‐cell gel electrophoresis: Loops and fragments

We investigated the mechanisms of DNA exit during single‐cell gel electrophoresis (the comet assay) by measuring the kinetics of the comet tail formation. In the neutral comet assay, the rate of DNA exit was found to be dependent on the topological state of DNA, which was influenced by either ethidium bromide or a low radiation dose. The results clearly show that the comet tail is formed by extended DNA loops: the loop extension, being reversible when the DNA torsional constraint remains in the loops, is favored when the constraint is relaxed. The kinetics of the comet formation in the case of a high radiation dose points out that accumulation of the single‐strand breaks causes DNA fragmentation. In contrast to the neutral comet assay, the alkaline comet assay is not related to the chromatin loops. Our results imply that the alkaline treatment induces detachment of the loops from the nuclear matrix, and the comet tail is formed by ssDNA fragments, the ends of which are pulled out from the comet head by electric force. We suggest that the kinetic approach can be considered as an important improvement of the comet assay.     

DNA SYNTHESIS-KINETICS, CELL DIVISION DELAY, AND POST-REPLICATION REPAIR AFTER UV IRRADIATION OF FROZEN CELLS OF E. COLI B/r

Abstract— Previous studies have shown that the relative yields of photoproducts produced in the DNA of Escherichia coli cells UV irradiated at -79°C differ from those produced at +21°C; the yield of DNA-protein cross-links was markedly enhanced at -79°C while the yield of thymine dimers was reduced. In the present studies, cells of E. coli B/r thy were frozen at -79°C, and then UV irradiated (254nm) while frozen(4.7 J m^-2), or after thawing (22 Jm^-2). Essentially the same survival, cell division delay, and DNA synthesis kinetics were observed for these two samples after irradiation, even though the UV fluence differed by a factor of ˜5. This supports previous observations that a correlation exists between the magnitude of the effects of UV radiation upon DNA synthesis kinetics and on cell survival. The weight average molecular weight of the pulse labeled DNA in the sample irradiated at +21°C was one-half that of the sample irradiated at -79°C, and complete repair of daughter-strand gaps was observed in both cases. Thus, UV-induced lesions produced in cells at -79°C (i.e. DNA-protein cross-links) appear to be amenable to post-replicational repair. While the overall DNA synthesis kinetics were the same for the two irradiation procedures, the apparent number of lesions produced per unit length of DNA was not. This suggests that each of the lesions produced in frozen cells, although apparently fewer in number, must cause a longer local delay in DNA synthesis than those lesions produced at +21°C.