Photoreactive DNA as a Tool to Study Replication Protein A Functioning in DNA Replication and Repair

Replication protein A (RPA), eukaryotic single-stranded DNA-binding protein, is a key player in multiple processes of DNA metabolism including DNA replication, recombination and DNA repair. Human RPA composed of subunits of 70-, 32- and 14-kDa binds ssDNA with high affinity and interacts specifically with multiple proteins. The RPA heterotrimer binds ssDNA in several modes, with occlusion lengths of 8–10, 13–22 and 30 nucleotides corresponding to global, transitional and elongated conformations of protein. Varying the structure of photoreactive DNA, the intermediates of different stages of DNA replication or DNA repair were designed and applied to identify positioning of the RPA subunits on the specific DNA structures. Using this approach, RPA interactions with various types of DNA structures attributed to replication and DNA repair intermediates were examined. This review is dedicated to blessed memory of Prof. Alain Favre who contributed to the development of photoreactive nucleotide derivatives and their application for the study of protein–nucleic acids interactions.     

The electronic effects of substituents at the acyl carbon in the gas-phase elimination kinetics of tert-butyl α-substituted acetates

The gas-phase eliminations of several tert-butyl esters, in a static system and in vessels seasoned with allyl bromide, have been studied in the temperature range of 171.5–280.1°C and the pressure range of 23–98 torr. The rate coefficients for the homogeneous unimolecular elimination of these esters are given by the following Arrhenius equations: for tert-butyl pivalate, log k₁(s^?1) = (13.44 ± 0.30) ? (169.1 ± 3.1) kJ · mol^?1 (2.303RT)^?1; for tert-butyl trichloroacetate, log k₁(s^?1) = (12.41 ± 0.08) ? (141.1 ± 0.7) kJ · mol^?1 (2.303RT)^?1; and for tert-butyl cyanoacetate log k₁(s^?1) = (11.31 ± 0.44) ? (137.8 ± 4.1) kJ · mol^?1 (2.303RT)^?1. The data of this work together with those reported in the literature yield a good linear relationship when plotting log k/k₀ vs. σ* values (ρ* = 0.635, correlation coefficient r = 0.972, and intercept = 0.048 at 250°C). The positive ρ* value suggests that the movement of negative charge to the acyl carbon in the transition state is rate determining. The present results along with previous investigations ratify the generalization that electron-withdrawing substituents at the acyl side of ethyl, isopropyl, and tert-butyl esters enhance the elimination rates, while electron-releasing groups tend to reduce them. The negative nature of the acyl carbon and the polarity in the transition state increases slightly from primary to tertiary esters.     

Existence, uniqueness, and quenching properties of solutions for degenerate semilinear parabolic problems with second boundary conditions

Let q?0, p?0, T?∞, D=(0,a), , Ω=D×(0,T), and Lu=xqut−uxx. This article considers the following degenerate semilinear parabolic initial-boundary value problem,

     

PNIPAAM Grafted Polymeric Monoliths Synthesized by the Reactive Gelation Process and their Swelling/Deswelling Characteristics

The production of macroporous monoliths functionalized with a thermo‐responsive polymer (PNIPAAM) is described. The surface functionalization was achieved by copolymerization of acrylic end capped atom transfer radical polymerization initiator (BPOEA) with divinylbenzene with or without styrene. Monoliths were generated by swelling them with styrene, BPOEA and divinylbenzene followed by gelation with salt and post polymerization. Subsequent grafting of these monoliths with PNIPAAM was achieved by atom transfer radical polymerization and their swelling deswelling characteristics quantified. The grafted monoliths provide a unique chromatographic stationary phase where adsorption/desorption can be driven by the use of temperature only.

     

Chemically stable films for combinatorial fluorosensor arrays

Sensor arrays are useful for many purposes. Our interests include quasi-distributed intrinsic fiber optic arrays, those distributed along the length of an optical fiber. We have demonstrated an optical time-of-flight approach to distinguishing the fluorescence output of such arrays, as well as a synthesis of combinatorial libraries that takes advantage of a support of linear morphology to make numerous compounds in a simple manner without information loss in the synthesis. To unite these research areas, we needed an optical fiber cladding material that meets demanding synthetic and optical requirements. We have chosen the Meldal SPOCC polymer support as the best candidate for such a material and report here our initial results with this material.     

A PDE Approach to the Prediction of a Binary Sequence with Advice from Two History-Dependent Experts

The prediction of a binary sequence is a classic example of online machine learning. We like to call it the “stock prediction problem,” viewing the sequence as the price history of a stock that goes up or down one unit at each time step. In this problem, an investor has access to the predictions of two or more “experts,” and strives to minimize her final-time regret with respect to the best-performing expert. Probability plays no role; rather, the market is assumed to be adversarial. We consider the case when there are two history-dependent experts, whose predictions are determined by the d most recent stock moves. Focusing on an appropriate continuum limit and using methods from optimal control, graph theory, and partial differential equations, we discuss strategies for the investor and the adversarial market, and we determine associated upper and lower bounds for the investor's final-time regret. When d ≤ 4 our upper and lower bounds coalesce, so the proposed strategies are asymptotically optimal. Compared to other recent applications of partial differential equations to prediction, ours has a new element: there are two timescales, since the recent history changes at every step whereas regret accumulates more slowly. © 2022 Wiley Periodicals LLC.     

Shear ordered diblock copolymers with tuneable optical properties

A series of high molecular weight poly(styrene-b-isoprene) block copolymers with optical properties defined by composition in a non-selective solvent were studied using simultaneous ultra small angle X-ray scattering (USAXS) and optical spectrometry. A small magnitude shear produces ordered and oriented states in the copolymer solutions that persist for extended periods of time, and also have superior optical properties that are directly attributable to the mesoscopic block copolymer (BCP) morphology. We have demonstrated that the optical transmission of these materials can be tuned by the addition of low molecular weight poly(isoprene) and poly(styrene) to swell their respective domains within the diblock copolymer. The optical transmission peak for the diblocks could be tuned; from 380 nm-440 nm for the 670k diblock, 425 nm-540 nm for the 850k diblock and 541 nm-625 nm for the 1 million diblock by altering the solution concentration and composition. The full width at half maximum that can be achieved for the optical transmission peaks is as small as 15 nm at 473 nm with a Δλ/λ of 0.03, highlighting the high quality ordering in these systems. Also a small shift in the transmission peak wavelength was observed across a wide angle of view (15 nm at 30°) suggesting that these materials could be used for large area narrow band optical filters.     

Electroless deposition of gold into poly-3,4-ethylenedioxythiophene films and their characterization performed in chloride-containing solutions

Au-containing polymer films were obtained by electroless deposition of gold from diluted solutions of HAuCl₄ into preliminarily reduced poly-3,4-ethylenedioxythiophene (PEDOT) films. Structural peculiarities of such pristine and composite films were characterized by scanning and transmission electron microscopy methods. It was established that the gold clusters forming under such deposition appear on the outer surface of polymer films and their pores. The clusters’ sizes ranged between 30 and 100 nm depending on the time of exposition of a PEDOT film in solutions of Au(III) ions and the concentration of these ions. It was also observed that in contrast to pristine PEDOT films, cyclic voltammograms (CVs) of composite films in the presence of chloride ions show additional redox peaks resulting from oxidation of gold with formation of an insoluble product and followed by the product reduction under reversal of the potential scan direction. As a result of parallel electrochemical quartz crystal microbalance (EQCM) and CV measurements, it was also established that the number of chloride ions per one transferring electron in the gold oxidation process is near to unity. To elucidate the oxidation degree of gold in the presence of chloride ions, a special procedure of changing the electrode potential was used. It consisted of clamping the high anodic potential in the region of gold oxidation (0.97 V, Ag/AgCl) and subsequent gradual decrease of the electrode potential with a constant scan rate. Under these conditions, it was possible to completely oxidize all the gold particles containing in a composite film and find out the maximum amount of electricity consumed for the product particles’ reduction. A comparison between such data and the results obtained in EQCM determinations of the gold content in the same film led to the conclusion that the oxidation state of gold in the complexes formed is Au(III). The effects of chloride ion concentration and scan rate of the electrode potential on current responses of PEDOT–Au films were investigated. Some primary conclusions on the kinetics of the studied processes are made.