scholarly journals Transient kinetics measured with force steps discriminate between double-stranded DNA elongation and melting and define the reaction energetics

2013 ◽  
Vol 42 (5) ◽  
pp. 3436-3449 ◽  
Author(s):  
Lorenzo Bongini ◽  
Luca Melli ◽  
Vincenzo Lombardi ◽  
Pasquale Bianco
Keyword(s):  
Entropy Change ◽  
Structural Factors ◽  
Transient Kinetics ◽  
Double Stranded Dna ◽  
Phage Dna ◽  
Thermal Melting ◽  
Kinetics Of ◽  
Entropic Contribution ◽  
Force Drop

Abstract Under a tension of ∼65 pN, double-stranded DNA undergoes an overstretching transition from its basic (B-form) conformation to a 1.7 times longer conformation whose nature is only recently starting to be understood. Here we provide a structural and thermodynamic characterization of the transition by recording the length transient following force steps imposed on the λ-phage DNA with different melting degrees and temperatures (10–25°C). The shortening transient following a 20–35 pN force drop from the overstretching force shows a sequence of fast shortenings of double-stranded extended (S-form) segments and pauses owing to reannealing of melted segments. The lengthening transients following a 2–35 pN stretch to the overstretching force show the kinetics of a two-state reaction and indicate that the whole 70% extension is a B-S transition that precedes and is independent of melting. The temperature dependence of the lengthening transient shows that the entropic contribution to the B-S transition is one-third of the entropy change of thermal melting, reinforcing the evidence for a double-stranded S-form that maintains a significant fraction of the interstrand bonds. The cooperativity of the unitary elongation (22 bp) is independent of temperature, suggesting that structural factors, such as the nucleic acid sequence, control the transition.

scholarly journals Transient kinetic analysis of oxidative dealkylation by the direct reversal DNA repair enzyme AlkB

2020 ◽  
Vol 295 (21) ◽  
pp. 7317-7326 ◽  
Author(s):  
Michael R. Baldwin ◽  
Suzanne J. Admiraal ◽  
Patrick J. O'Brien
Keyword(s):  
Dna Repair ◽  
Alkylating Agents ◽  
Transient Kinetics ◽  
Repair Enzyme ◽  
Future Studies ◽  
Dna And Rna ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Kinetic Mechanisms ◽  
Kinetics Of

AlkB is a bacterial Fe(II)– and 2-oxoglutarate–dependent dioxygenase that repairs a wide range of alkylated nucleobases in DNA and RNA as part of the adaptive response to exogenous nucleic acid–alkylating agents. Although there has been longstanding interest in the structure and specificity of Escherichia coli AlkB and its homologs, difficulties in assaying their repair activities have limited our understanding of their substrate specificities and kinetic mechanisms. Here, we used quantitative kinetic approaches to determine the transient kinetics of recognition and repair of alkylated DNA by AlkB. These experiments revealed that AlkB is a much faster alkylation repair enzyme than previously reported and that it is significantly faster than DNA repair glycosylases that recognize and excise some of the same base lesions. We observed that whereas 1,N6-ethenoadenine can be repaired by AlkB with similar efficiencies in both single- and double-stranded DNA, 1-methyladenine is preferentially repaired in single-stranded DNA. Our results lay the groundwork for future studies of AlkB and its human homologs ALKBH2 and ALKBH3.

Irradiation behavior of pyrolytic silicon carbide

1983 ◽  
Vol 41 ◽  
pp. 72-73
Author(s):  
R. J. Lauf
Keyword(s):  
Silicon Carbide ◽  
Fission Products ◽  
Thermodynamics And Kinetics ◽  
Neutron Fluences ◽  
Fuel Particles ◽  
Sic Coatings ◽  
Irradiation Behavior ◽  
Kinetics Of ◽  
Htgr Fuel

Fuel particles for the High-Temperature Gas-Cooled Reactor (HTGR) contain a layer of pyrolytic silicon carbide to act as a miniature pressure vessel and primary fission product barrier. Optimization of the SiC with respect to fuel performance involves four areas of study: (a) characterization of as-deposited SiC coatings; (b) thermodynamics and kinetics of chemical reactions between SiC and fission products; (c) irradiation behavior of SiC in the absence of fission products; and (d) combined effects of irradiation and fission products. This paper reports the behavior of SiC deposited on inert microspheres and irradiated to fast neutron fluences typical of HTGR fuel at end-of-life.

Elaboration and Characterization of the Properties of Refractory Cr Base Alloys

2010 ◽  
Vol 72 ◽  
pp. 46-52 ◽  
Author(s):  
Laurent Royer ◽  
Stéphane Mathieu ◽  
Christophe Liebaut ◽  
Pierre Steinmetz
Keyword(s):  
Mechanical Properties ◽  
Melting Point ◽  
Molten Glass ◽  
Energy Production ◽  
Creep Properties ◽  
Refractory Alloys ◽  
Industrial Use ◽  
Kinetics Of ◽  
Selection Of

For energy production and also for the glass industry, finding new refractory alloys which could permit to increase the process temperatures to 1200°C or more is a permanent challenge. Chromium base alloys can be good candidates, considering the melting point of Cr itself, and also its low corrosion rate in molten glass. Two families of alloys have been studied for this purpose, Cr-Mo-W and Cr-Ta-X alloys (X= Mo, Si..). A finer selection of compositions has been done, to optimize their chemical and mechanical properties. Kinetics of HT oxidation by air, of corrosion by molten glass and also creep properties of several alloys have been measured up to 1250°C. The results obtained with the best alloys (Cr-Ta base) give positive indications as regards the possibility of their industrial use.

scholarly journals New Trimethoprim-Like Molecules: Bacteriological Evaluation and Insights into Their Action

Antibiotics ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 709
Author(s):  
Marta Jorba ◽  
Marina Pedrola ◽  
Ouldouz Ghashghaei ◽  
Rocío Herráez ◽  
Lluis Campos-Vicens ◽  
...  
Keyword(s):  
Inhibitory Concentration ◽  
Efflux Pump ◽  
Synergistic Effects ◽  
Nicotinamide Adenine Dinucleotide Phosphate ◽  
Detailed Characterization ◽  
Low Concentrations ◽  
Pump Activity ◽  
Bacteriological Evaluation ◽  
Kinetics Of

This work reports a detailed characterization of the antimicrobial profile of two trimethoprim-like molecules (compounds 1a and 1b) identified in previous studies. Both molecules displayed remarkable antimicrobial activity, particularly when combined with sulfamethoxazole. In disk diffusion assays on Petri dishes, compounds 1a and 1b showed synergistic effects with colistin. Specifically, in combinations with low concentrations of colistin, very large increases in the activities of compounds 1a and 1b were determined, as demonstrated by alterations in the kinetics of bacterial growth despite only slight changes in the fractional inhibitory concentration index. The effect of colistin may be to increase the rate of antibiotic entry while reducing efflux pump activity. Compounds 1a and 1b were susceptible to extrusion by efflux pumps, whereas the inhibitor phenylalanine arginyl β-naphthylamide (PAβN) exerted effects similar to those of colistin. The interactions between the target enzyme (dihydrofolate reductase), the coenzyme nicotinamide adenine dinucleotide phosphate (NADPH), and the studied molecules were explored using enzymology tools and computational chemistry. A model based on docking results is reported.

scholarly journals Simultaneous Kinetics of Selenite Oxidation and Sorption on δ-MnO2 in Stirred-Flow Reactors

2021 ◽  
Vol 18 (6) ◽  
pp. 2902
Author(s):  
Zheyong Li ◽  
Yajun Yuan ◽  
Lin Ma ◽  
Yihui Zhang ◽  
Hongwei Jiang ◽  
...  
Keyword(s):  
Rate Constant ◽  
Photoelectron Spectroscopy ◽  
Oxide Surfaces ◽  
Kinetic Rate Constant ◽  
Flow Reactors ◽  
Mn Oxide ◽  
Remediation Strategies ◽  
Process Of Se ◽  
Kinetics Of

Selenium (Se) is an essential and crucial micronutrient for humans and animals, but excessive Se brings negativity and toxicity. The adsorption and oxidation of Se(IV) on Mn-oxide surfaces are important processes for understanding the geochemical fate of Se and developing engineered remediation strategies. In this study, the characterization of simultaneous adsorption, oxidation, and desorption of Se(IV) on δ-MnO2 mineral was carried out using stirred-flow reactors. About 9.5% to 25.3% of Se(IV) was oxidized to Se(VI) in the stirred-flow system in a continuous and slow process, with the kinetic rate constant k of 0.032 h−1, which was significantly higher than the apparent rate constant of 0.0014 h−1 obtained by the quasi-level kinetic fit of the batch method. The oxidation reaction was driven by proton concentration, and its rate also depended on the Se(IV) influent concentration, flow rate, and δ-MnO2 dosage. During the reaction of Se(IV) and δ-MnO2, Mn(II) was produced and adsorbed strongly on Mn oxide surfaces, which was evidenced by the total reflectance Fourier transform infrared (ATR-FTIR) results. The X-ray photoelectron spectroscopy (XPS) data indicated that the reaction of Se(VI) on δ-MnO2 produced Mn(III) as the main product. These results contribute to a deeper understanding of the interface chemical process of Se(IV) with δ-MnO2 in the environment.

scholarly journals Synthesis and Polymerization Kinetics of Rigid Tricyanate Ester

Polymers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1686
Author(s):  
Andrey Galukhin ◽  
Roman Nosov ◽  
Ilya Nikolaev ◽  
Elena Melnikova ◽  
Daut Islamov ◽  
...  
Keyword(s):  
Kinetic Analysis ◽  
Single Step ◽  
Polymerization Kinetics ◽  
Scanning Calorimetry ◽  
Modulated Differential Scanning Calorimetry ◽  
Diffusion Controlled ◽  
Polymerization Product ◽  
The One ◽  
Kinetics Of

A new rigid tricyanate ester consisting of seven conjugated aromatic units is synthesized, and its structure is confirmed by X-ray analysis. This ester undergoes thermally stimulated polymerization in a liquid state. Conventional and temperature-modulated differential scanning calorimetry techniques are employed to study the polymerization kinetics. A transition of polymerization from a kinetic- to a diffusion-controlled regime is detected. Kinetic analysis is performed by combining isoconversional and model-based computations. It demonstrates that polymerization in the kinetically controlled regime of the present monomer can be described as a quasi-single-step, auto-catalytic, process. The diffusion contribution is parameterized by the Fournier model. Kinetic analysis is complemented by characterization of thermal properties of the corresponding polymerization product by means of thermogravimetric and thermomechanical analyses. Overall, the obtained experimental results are consistent with our hypothesis about the relation between the rigidity and functionality of the cyanate ester monomer, on the one hand, and its reactivity and glass transition temperature of the corresponding polymer, on the other hand.

scholarly journals Structural Factors Inducing Cracking of Brass Fittings

Materials ◽  
2021 ◽  
Vol 14 (12) ◽  
pp. 3255
Author(s):  
Lenka Kunčická ◽  
Michal Jambor ◽  
Adam Weiser ◽  
Jiří Dvořák
Keyword(s):  
Chemical Composition ◽  
Plastic Flow ◽  
Beta Phase ◽  
Alpha Phase ◽  
Structural Factors ◽  
Transmission Electron ◽  
Medical Gas ◽  
Hot Die Forging ◽  
Multiple Step

Cu–Zn–Pb brasses are popular materials, from which numerous industrially and commercially used components are fabricated. These alloys are typically subjected to multiple-step processing—involving casting, extrusion, hot forming, and machining—which can introduce various defects to the final product. The present study focuses on the detailed characterization of the structure of a brass fitting—i.e., a pre-shaped medical gas valve, produced by hot die forging—and attempts to assess the factors beyond local cracking occurring during processing. The analyses involved characterization of plastic flow via optical microscopy, and investigations of the phenomena in the vicinity of the crack, for which we used scanning and transmission electron microscopy. Numerical simulation was implemented not only to characterize the plastic flow more in detail, but primarily to investigate the probability of the occurrence of cracking based on the presence of stress. Last, but not least, microhardness in specific locations of the fitting were examined. The results reveal that the cracking occurring in the location with the highest probability of the occurrence of defects was most likely induced by differences in the chemical composition; the location the crack in which developed exhibited local changes not only in chemical composition—which manifested as the presence of brittle precipitates—but also in beta phase depletion. Moreover, as a result of the presence of oxidic precipitates and the hard and brittle alpha phase, the vicinity of the crack exhibited an increase in microhardness, which contributed to local brittleness.

scholarly journals Biosorption and Diffusion Modeling of Pb(II) by Malt Bagasse

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Klaiani B. Fontana ◽  
Giane Gonçalves Lenzi ◽  
Erica R. L. R. Watanabe ◽  
Ervin Kaminski Lenzi ◽  
Juliana A. M. T. Pietrobelli ◽  
...  
Keyword(s):  
Sorption Process ◽  
Isotherm Models ◽  
Diffusion Modeling ◽  
Biosorption Capacity ◽  
Kinetic And Thermodynamic Parameters ◽  
Pseudo Second Order ◽  
Ph Optimization ◽  
Kinetics Of ◽  
And Diffusion

The removal of Pb(II) from water by biosorption processes onto malt bagasse was investigated and the kinetic and thermodynamic parameters were obtained; additionally a diffusion modeling was proposed. The characterization of malt bagasse was performed by FTIR and SEM/EDS. The experiments were conducted in batch system and an experimental design based response surface methodology was applied for agitation speed and pH optimization. The kinetics of biosorption followed pseudo-second-order model and the temperature of the process affected the biosorption capacity. Isotherm models of Langmuir, Freundlich, and Elovich were applied and the Langmuir model showed better fit and the estimated biosorption capacity was 29.1 mg g−1. The negative values obtained for ΔG° and positive values of ΔH° confirm, respectively, the spontaneous and endothermic nature of the process. The diffusion modeling was performed based on experiments in the absence of agitation to investigate the influence of the biosorbent on the sorption process of Pb(II) ions.

scholarly journals High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Betty Ha ◽  
Kevin P. Larsen ◽  
Jingji Zhang ◽  
Ziao Fu ◽  
Elizabeth Montabana ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Viral Entry ◽  
Reverse Transcription ◽  
Molecular Mechanisms ◽  
Dissociation Kinetics ◽  
Structural Mechanism ◽  
Medium Resolution ◽  
Kinetics Of ◽  
Hiv 1

AbstractReverse transcription of the HIV-1 viral RNA genome (vRNA) is an integral step in virus replication. Upon viral entry, HIV-1 reverse transcriptase (RT) initiates from a host tRNALys3 primer bound to the vRNA genome and is the target of key antivirals, such as non-nucleoside reverse transcriptase inhibitors (NNRTIs). Initiation proceeds slowly with discrete pausing events along the vRNA template. Despite prior medium-resolution structural characterization of reverse transcriptase initiation complexes (RTICs), higher-resolution structures of the RTIC are needed to understand the molecular mechanisms that underlie initiation. Here we report cryo-EM structures of the core RTIC, RTIC–nevirapine, and RTIC–efavirenz complexes at 2.8, 3.1, and 2.9 Å, respectively. In combination with biochemical studies, these data suggest a basis for rapid dissociation kinetics of RT from the vRNA–tRNALys3 initiation complex and reveal a specific structural mechanism of nucleic acid conformational stabilization during initiation. Finally, our results show that NNRTIs inhibit the RTIC and exacerbate discrete pausing during early reverse transcription.

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