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A small circular DNA - plasmid pBR322, is considered as a complex dynamic system where nonlinear conformational perturbations which are often named open states or kinks, can arise and propagate. To describe the internal dynamics of the plasmid we use mathematical model consisting of two coupled sine-Gordon equations that in the average field approximation are transformed to two sine-Gordon independent equations with renormalized coefficients. The first equation describes angular oscillations of nitrous bases of the main chain. The second equation describes angular oscillations of nitrous bases in the complementary chain. As a result, two types of kink-like solutions have been obtained. One type kinks were the solutions of the first equation, and the other kinks were the solutions of the second equation. We calculated the main characteristics of the kink motion, including the time dependences of the kink velocity, coordinates, and total energy. These calculations were performed at the initial velocity equal to 1881 m/s which was chosen to avoid reflections from energy barriers corresponding to CDS-1 and CDS-2. The movement of the kinks was investigated by the method of the double energy profile. The maximum complete set of the DNA dynamic parameters was used to calculate the double profile. To calculate the velocity, energy and trajectory of the kinks, the block method was used. The results obtained made it possible to explain in which region of the plasmid the formation of a transcription bubble is most likely, as well to understand in which direction the bubble will move and the transcription process will go.

A small circular DNA - plasmid pBR322, is considered as a complex dynamic system where nonlinear conformational perturbations which are often named open states or kinks, can arise and propagate. To describe the internal dynamics of the plasmid we use mathematical model consisting of two coupled sine-Gordon equations that in the average field approximation are transformed to two sine-Gordon independent equations with renormalized coefficients. The first equation describes angular oscillations of nitrous bases of the main chain. The second equation describes angular oscillations of nitrous bases in the complementary chain. As a result, two types of kink-like solutions have been obtained. One type kinks were the solutions of the first equation, and the other kinks were the solutions of the second equation. We calculated the main characteristics of the kink motion, including the time dependences of the kink velocity, coordinates, and total energy. These calculations were performed at the initial velocity equal to 1881 m/s which was chosen to avoid reflections from energy barriers corresponding to CDS-1 and CDS-2. The movement of the kinks was investigated by the method of the double energy profile. The maximum complete set of the DNA dynamic parameters was used to calculate the double profile. To calculate the velocity, energy and trajectory of the kinks, the block method was used. The results obtained made it possible to explain in which region of the plasmid the formation of a transcription bubble is most likely, as well to understand in which direction the bubble will move and the transcription process will go. [ABSTRACT FROM AUTHOR]

Abstract—Conformational mobility is one of the most important properties of the DNA molecule. A striking example of this mobility is provided by the formation of regions where the double helix is locally unwound. The resulting so-called open DNA states play an important role in transcription, replication, and denaturation. In a "nonrelativistic" approximation, the open DNA states are often modeled as quasiparticles, or kinks, with a certain mass (mk), velocity (uk), and rest energy (E0 k). When more than one open state forms in a DNA molecule, statistics can be considered for an ensemble of N DNA kinks. The statistical properties of the ensemble are still poorly understood. In this paper the properties were investigated on the basis of recent data on the dynamic characteristics of DNA kinks. It was assumed that the interaction between the kinks is weak, all kinks are identical and the number N of DNA kinks is fixed. The statistical sum Zk, the free energy Fk, the velocity distribution function ρ1(vk), the average energy εk, the heat capacity Cv, k, and the entropy Sk were calculated for the ensemble of N DNA kinks. Temperature dependence curves of these characteristics were obtained and compared for four homogeneous sequences (poly(A), poly(T), poly(G), and poly(C)) and the pBR322 plasmid sequence. [ABSTRACT FROM AUTHOR]

A highly effective strategy for quantification of plasmid which was a special dsDNA based on bisPNA by electrochemical impedance spectroscopy was presented in this work. Firstly, through Au−S bond, thiol‐terminated bisPNA probes were immobilized onto the gold electrode surface. Then bisPNA probes directly hybridized with target plasmid DNA pBR322 based on the PNA.DNA‐PNA invasion triplex without denaturation. In the presence of redox electroactive ions [Fe(CN)6]3−/4− as hybridization indicator, the charge transfer resistance (Rct) was produced, and Rct was measured via electrochemical impedance spectroscopy. Under optimal conditions, this strategy showed a good linear relationship between the ΔRct which was the difference of Rct obtained before and after bisPNA hybridized with plasmid pBR322, and logarithm of the concentration of plasmid pBR322 within the range from 1 nM to 100 nM (R2=0.993), with a limit of detection (LOD) of 0.1 nM. Furthermore, this bisPNA‐assisted biosensor showed good stability and satisfactory analytical reliability. In addition, this novel bisPNA‐assisted biosensor also exhibited excellent analytical results in human serum. [ABSTRACT FROM AUTHOR]

Intensive use of chemical pesticides in agriculture poses environmental risks and may have negative impacts on agricultural productivity. The potential phytotoxicity of two chemical pesticides, chlorpyrifos (CPS) and fensulfothion (FSN), were evaluated using Cicer arietinum and Allium cepa as model crops. Different concentrations (0–100 μgmL-1) of both CPS and FSN decreased germination and biological attributes of C. arietinum. High pesticide doses significantly (p ≤ 0.05) caused membrane damage by producing thiobarbituric acid reactive substances (TBARS) and increasing proline (Pro) content. Pesticides elevated ROS levels and substantially increased the superoxide anions and H 2 O 2 concentrations, thus aggravating cell injury. Plants exposed to high pesticide dosages displayed significantly higher antioxidant levels to combat pesticide-induced oxidative stress. Ascorbate peroxidase (APX), guaiacol peroxidase (GPX), catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) increased by 48%, 93%, 71%, 52% and 94%, respectively, in C. arietinum roots exposed to 100 µgFSNmL-1. Under CLSM, pesticide-exposed C. arietinum and 2',7'-dichlorodihydrofluorescein diacetate (2'7'-DCF) and 3,3'-diaminobenzidine stained roots exhibited increased ROS production in a concentration-dependent manner. Additionally, enhanced Rhodamine 123 (Rhd 123) and Evan's blue fluorescence in roots, as well as changes in mitochondrial membrane potential (ΔΨ m) and cellular apoptosis, were both associated with high pesticide dose. Allium cepa chromosomal aberration (CAs) assay showed a clear reduction in mitotic index (MI) and numerous chromosomal anomalies in root meristematic cells. Additionally, a-dose-dependent increase in DNA damage in root meristematic cells of A. cepa and conversion of the super-coiled form of DNA to open circular in pBR322 plasmid revealed the genotoxic potential of pesticides. The application of CPS and FSN suggests phytotoxic and cyto-genotoxic effects that emphasize the importance of careful monitoring of current pesticide level in soil before application and addition at optimal levels to soil-plant system. It is appropriate to prepare both target-specific and slow-release agrochemical formulations for crop protection with concurrent safeguarding of agroecosystems. • Pesticides significantly affected germination and biometric parameters of Cicer arietinum. • Pesticides caused alteration in mitochondrial membrane potential (ΔΨm) and cellular death in C. arietinum roots. • Pesticide dose-dependent increase in antioxidant enzymes was recorded. • Cytotoxicity and genotoxicity of pesticides was evaluated. • Pesticides caused DNA disintegration in Allium cepa and damage in plasmid pBR322. [ABSTRACT FROM AUTHOR]

The reactions of hydroxyl and glutathiyl radicals with dehydrogingerdione (1) have been studied using biochemical assays and the pulse radiolysis technique in order to understand its radioprotective and antioxidant action. It was found to inhibit the Fenton-mediated 2-deoxyribose oxidation, as well as γ-ray-induced plasmid DNA strand breaks in a concentration-dependent fashion. The pulse radiolysis studies revealed its high reactivity with the hydroxyl and glutathiyl radicals. With the hydroxyl radicals, it initially formed three species, an adduct, a phenoxyl and a methylenic radical. The bimolecular rate constants for the formation of these species were the same (approx. 6.8 × 109 dm3/mol per s). The initially formed adduct also produced the phenoxyl radical at a later stage. In the case of glutathiyl-radical-induced oxidation, an adduct at the α–β double bond was formed as the sole species. Its identity as a carbon-centered radical was inferred from the result of the oxygen effect on the decay of the adduct radical. At a later stage, the adduct radical also produced the phenoxyl radical through an intramolecular radical transformation. A suitable mechanism for the oxidation reactions of 1 has been proposed. [ABSTRACT FROM AUTHOR]