Influence of different energy drains on the interrelationship between the rate of respiration,proton-motive force and adenine nucleotide patterns in isolated mitochondria

The respiration of rat liver mitochondria was stimulated by three different ways of energy drain: (a) partial uncoupling (equivalent to direct collapse of the proton-motive force), (b) intramitochondrial utilization of ATP for citrulline synthesis, and (c) extramitochondrial utilization of ATP for glucose phosphorylation. At identical rates of respiration, the intramitochondrial ATP: ADP ratios were the same in all three systems. Furthermore, the proton-motive force was the same in partially uncoupled mitochondria and in the presence of hexokinase plus glucose up to a respiration rate amounting to about 60% of that of the fully active state. However, external ATP: ADP ratios were considerably different in various systems at comparable rates of oxygen uptake, being the lowest under conditions when ATP was being utilized externally. On this basis, it is concluded that the respiratory rate is controlled directly by the proton-motive force and the mitochondrial ATP-synthesizing system operates under near-equilibrium conditions with respect to the membrane energy state parameters. However, a disequilibrium exists at the step of the transport of ATP from mitochondria to the external (cytoplasmic) compartment.     

Evolution of Hot Polaron States with a Nanosecond Lifetime in a Manganite Perovskite

Understanding and controlling the relaxation process of optically excited charge carriers in solids with strong correlations is of great interest in the quest for new strategies to exploit solar energy. Usually, optically excited electrons in a solid thermalize rapidly on a femtosecond to picosecond timescale due to interactions with other electrons and phonons. New mechanisms to slow down thermalization will thus be of great significance for efficient light energy conversion, e.g., in photovoltaic devices. Ultrafast optical pump–probe experiments in the manganite Pr_0.65Ca_0.35MnO_3, a photovoltaic, thermoelectric, and electrocatalytic material with strong polaronic correlations, reveal an ultraslow recombination dynamics on a nanosecond‐time scale. The nature of long living excitations is further elucidated by photovoltaic measurements, showing the presence of photodiffusion of excited electron–hole polaron pairs. Theoretical considerations suggest that the excited charge carriers are trapped in a hot polaron state. Escape from this state is possible via a slow dipole‐forbidden recombination process or via rare thermal fluctuations toward a conical intersection followed by a radiation‐less decay. The strong correlation between the excited polaron and the octahedral dynamics of its environment appears to be substantial for stabilizing the hot polaron.     

Photophysics of ANS. IV. Electron transfer quenching of ANS in alcoholic solvents and mixtures

ANS is observed to decay from the fluorescent state with distributed kinetics in nearly pure ethanol solvent, notwithstanding that in mixed ethanol/water solvents the decay is discrete and biexponential. The origin of this behavior is investigated. In particular, a theory of electron transfer theory in the adiabatic regime is adduced, with specific involvement of solvent cage structure in the form of the solvent-electron polaron wave function. Properties of various polarons for various solvent systems are predicted and, for the case of ethanol and cyclohexanol, employed to generate the observed Arrhenius-type decay parameters in a quantitative fashion.     

Structural studies of E. coli topoisomerase III-DNA complexes reveal a novel type IA topoisomerase-DNA conformational intermediate

Escherichia coli DNA topoisomerase III belongs to the type IA family of DNA topoisomerases, which transiently cleave single-stranded DNA (ssDNA) via a 5' phosphotyrosine intermediate. We have solved crystal structures of wild-type E. coli topoisomerase III bound to an eight-base ssDNA molecule in three different pH environments. The structures reveal the enzyme in three distinct conformational states while bound to DNA. One conformation resembles the one observed previously with a DNA-bound, catalytically inactive mutant of topoisomerase III where DNA binding realigns catalytic residues to form a functional active site. Another conformation represents a novel intermediate in which DNA is bound along the ssDNA-binding groove but does not enter the active site, which remains in a catalytically inactive, closed state. A third conformation shows an intermediate state where the enzyme is still in a closed state, but the ssDNA is starting to invade the active site. For the first time, the active site region in the presence of both the catalytic tyrosine and ssDNA substrate is revealed for a type IA DNA topoisomerase, although there is no evidence of ssDNA cleavage. Comparative analysis of the various conformational states suggests a sequence of domain movements undertaken by the enzyme upon substrate binding.     

Analysis of DNA polymerase activity in Petunia protoplasts treated with clastogenic agents

Clastogenic agents, i.e. agents that can induce chromosome or DNA breakage, have been shown to enhance the rale of direct gene transfer to protoplasts. The effect was analysed at the enzymatic level using protoplast homogenates as well as intact protoplasts. For that purpose existing procedures were modified to enable measurement of DNA polymerase in vivo. In the system used, external DNA was able to enter the cells without the addition of membrane-permeabilizing compounds. When comparing total DNA polymerase activity of protoplasts irradiated with X-rays or UV-light with that of untreated cells we did not observe significant differences. Incubation of protoplasts with high doses of bleomycin affected total DNA polymerase activity negatively. but dideoxythymidine triphosphate-sensitive activity was not influenced. We conclude that the DNA strand-breaks induced by low doses of X-rays. UV-light or bleomycin do not increase the total or the repair-DNA polymerase activity and. therefore. that the increase in the transformation rates after DNA strand-breaking is not preceded by enhanced DNA polymerase activity.     

A new perspective on oxidation of DNA repair proteins and cancer

Reactive oxygen and nitrogen species (RONS) are formed as byproducts of many endogenous cellular processes, in response to infections, and upon exposure to various environmental factors. An increase in RONS can saturate the antioxidation system and leads to oxidative stress. Consequently, macromolecules are targeted for oxidative modifications, including DNA and protein. The oxidation of DNA, which leads to base modification and formation of abasic sites along with single and double strand breaks, has been extensively investigated. Protein oxidation is often neglected and is only recently being recognized as an important regulatory mechanism of various DNA repair proteins. This is a review of the current state of research on the regulation of DNA repair by protein oxidation with emphasis on the correlation between inflammation and cancer.     

DNA Repair Enzymes as Promising Targets in Oncotherapy

DNA repair is a complicated process that occurs due to a network of different pathways and mechanisms for correction of DNA damages during the normal DNA biosynthesis and under the influence of external and internal factors. The study of these mechanisms and their regulation is closely related to both diagnostics and the search for ways of treating various diseases, including oncological ones. Malignant neoplasms are one of the three most widespread diseases in the world, which unfortunately often become the reason for a lethal outcome. Traditional cancer therapy aims to the DNA damage in malignant cells, and its result depends on the efficiency of the repair systems. In many cancer cells, the individual DNA repair enzymes are overexpressed, which promotes the resistance of these tumors to the therapy. On the other hand, defects in the DNA repair systems in cancer cells allow researchers to find both appropriate biomarkers for diagnostics and targets for the development of the specific and effective therapy. Currently, DNA repair inhibitors are being actively developed in order to increase the sensitivity of the tumor cells to traditional chemotherapy. The principle of synthetic lethality is used to create cell-specific drugs and to improve the effectiveness of the treatment. In this review, we discuss the current state of research and prospects for the development of inhibitors for five important DNA repair enzymes.     

河北省沿海开发活动的生态环境效应评估

通过对河北省沿海开发活动及生态环境的分析,建立了由压力、状态、响应3个子系统28个指标组成的沿海开发活动的生态环境效应综合评估指标体系,采用综合指数法进行定量评价,并在此基础上构建了生态环境综合效应指数及其分级评判标准.结果表明： 1984—2010年,河北省沿海开发活动的生态环境效应呈现较小→一般→较大的变化,接受程度由可接受发展变为不可接受的水平.由于沿海开发利用所造成的资源、环境压力依然严峻,再加上状态对于响应的反应有一定滞后性,响应子系统各种措施的改善对状态的好转并没有表现出积极作用,海域质量状况呈现退化趋势.由于沿海各地开发方式和强度的差异,开发活动的生态环境效应呈现一定的空间差异,表现为秦皇岛沿海开发的生态环境效应最小,其次为沧州,唐山最大,且沧州和唐山都已达到不可接受的水平,需要进一步加强生态环境的恢复和保护工作.
     

Electron transfer between globular proteins. Evaluation of a matrix element

The dependence of the matrix element of the probability of interprotein electron transfer on the mutual orientation of the donor and acceptor centers and the distance between them was calculated. The calculations were made under the assumption that electron transfer proceeds mainly by a collective excitation of polaron nature, like a solvated electron state. The results obtained are consistent with experimental data and indicate the nonexponential behavior of this dependence in the case when the distance transfer is less than 20 A.     

Polaron stability in oligoacene crystals

The polaron stability in organic molecular crystals is theoretically investigated in the scope of a two-dimensional Holstein–Peierls model that includes lattice relaxation. Particularly, the investigation is focused on designing a model Hamiltonian that can address properly the polaron properties in different model oligoacene crystals. The findings showed that a suitable choice for a set of parameters can play the role of distinguishing the model crystals and, consequently, different properties related to the polaron stability in these systems are observed. Importantly, the usefulness of this model is stressed by investigating the electronic localization of the polaron, which provides a deeper understanding into the properties associated with the polaron stability in oligoacene crystals.     

Chemotherapeutic potential of 9-phenyl acridine: biophysical studies on its binding to DNA

Acridines and their derivatives are well-known probes for nucleic acids as well as being relevant in the field of drug development to establish new chemotherapeutic agents. We have shown from molecular modelling studies that 9-phenyl acridine and some of its derivatives can act as inhibitors of topoisomerase I and thus have potential to act as anticancer agents. Rational design of new compounds for therapeutics requires knowledge about their structural stability and interactions with various cellular macromolecules. In this regard it is important to know how these molecules would interact with DNA. Here we report the interaction of 9-phenyl acridine (ACPH) with calf thymus DNA (CT-DNA) based on various biophysical and molecular modelling studies. Spectrophotometric studies indicated that ACPH binds to CT-DNA. DNA melting studies revealed that binding of ACPH to CT-DNA resulted in a small increase in melting temperature, which is unlikely in case of classical intercalator; rather, it indicates external binding. Viscosity measurements show that ACPH exhibits groove binding. Competitive binding of ACPH to CT-DNA pre-bound to ethidium bromide (EB) showed slow quenching. Measurement of the binding constant of ACPH by fluorescent intercalator displacement (FID) assay corroborated the notion that there was groove binding. Molecular modelling studies also supported this finding. Results indicate that binding of ACPH is through partial intercalation in the minor groove of DNA.     

Effect of riboflavin and light on the secondary structure of DNA

S1 nuclease hydrolysis and benzoylated naphthoylated DEAE cellulose (BND-cellulose) chromatography have been used to study the effect of riboflavin and visible light on DNA. Native calf thymus DNA was incubated with riboflavin in the presence of fluorescent light for various time periods and subjected to S1 nuclease hydrolysis. An increasing degree of DNA degradation was seen suggesting a destabilization of the secondary structure. A decrease in melting temperature was also observed. Incubation with riboflavin and illumination caused adherence to BND-cellulose indicating the production of single stranded regions or breaks in the native double stranded molecules. However, when incubation was done in dark and in the presence of triplet excited state quencher, potassium iodide, a reduced adherence of DNA to BND-cellulose was seen. Plasmid pBR322 DNA was also treated with riboflavin under these conditions and subjected to agarose gel electrophoresis. No degradation could be seen in dark incubated and potassium iodide treated samples. These results indicate that the adherence of DNA to BND-cellulose in dark is possibly due to the binding of aromatic residues to the resin suggesting the formation of a complex between riboflavin and DNA.     

Charge Transport in Poly(dG)–Poly(dC) and Poly(dA)–Poly(dT) DNA Polymers

We investigate the charge transport in synthetic DNA polymers built up from single type of base pairs. In the context of a polaronlike model, for which an electronic tight-binding system and bond vibrations of the double helix are coupled, we present estimates for the electron-vibration coupling strengths utilizing a quantum-chemical procedure. Subsequent studies concerning the mobility of polaron solutions, representing the state of a localized charge in unison with its associated helix deformation, show that the system for poly(dG)–poly(dC) and poly(dA)–poly(dT) DNA polymers, respectively possess quantitatively distinct transport properties. While the former supports unidirectionally moving electron breathers attributed to highly efficient long-range conductivity, the breather mobility in the latter case is comparatively restrained, inhibiting charge transport. Our results are in agreement with recent experimental results demonstrating that poly(dG)–poly(dC) DNA molecules acts as a semiconducting nanowire and exhibit better conductance than poly(dA)–poly(dT) ones.     

大豆体细胞胚系培养及其微卫星DNA稳定性研究(简报)

植物离体培养是植物基因操作中的重要一环,也是植物个体发育研究中基因表达研究的有益参考体系。在继代培养过程中发生的遗传变异有时会使再生植株丧失优良的性状而需加以控制和避免。为此,首先需要了解培养过程中的遗传变异情况。     

Influence of periodic field with constant and slowly changing frequency on movement of DNA kink

The movement of a kink in homogeneous polynucleotide chains of DNA under the influence of three kinds of external periodic field—with constant, growing, and decreasing frequencies is investigated in the work. Dependences of speed and coordinate of the kink on time have been found with the help of McLaughlin and Scott energy method. Phase trajectories of the kink have been constructed. It has been shown that in the case of external action with constant frequency, the kink aspires to a limit cycle; in the case of an external field with increasing frequency it tends to a stationary state corresponding to a special point of stable focus type; in the case of an external field with decreasing frequency, the kink transfers from one stationary state (unstable focus) to another (stable focus). The obtained results show the possibility of governing the kink movement by slowly changing the frequency.     

Re-examination of the ColE1 DNA regions essential for autonomous replication and their functions

Starting from pAO3, a plasmid consisting of a quarter of colicinogenic factor E1 (ColE1) DNA, various small ColE1 derivatives were constructed by in vitro recombination and their ability to achieve autonomous replication was examined. The 436 base pair HaeIII-C fragment of pAO3 contained information for replication when it was recombined with the non-replicating Amp fragment. However, when it was connected to other DNA fragments, the resulting hybrid molecules were not isolated as plasmids. The present results indicate that the additional region of about 240 base pairs next to the HaeIII-C fragment of ColE1 is also essential for the maintenance of a plasmid state. Moreover, using various small ColE1 derivatives, the DNA region responsible for the interference and incompatibility functions of ColE1 DNAs was located. The results indicate that the interference and incompatibility functions are coded by the same ColE1 DNA segment and are not essential for the maintenance of a plasmid state.     

A DNA bank for people subjected to occupational irradiation. Goals and prospects

A DNA bank was created to preserve the genetic material of staff of the first Russian atomic plant, Production Association (PO) Mayak, who were exposed to chronic external gamma-irradiation at various doses in the early years of plant operation. Some of the workers experienced combined irradiation from external and internal (incorporated plutonium-239) sources. The unique genetic material of the subjects and their children can be used to study the remote consequences of irradiation by means of modern molecular-genetic techniques. At present, the bank contains the genetic material of 500 people. A database was constructed to include medical, demographic, professional, and dose characteristics of each individual and quantitative and qualitative parameters of each DNA preparation. The bank is continuously augmented with new DNA samples of the irradiated people and members of their families.