Determination of the energy characteristics of the reactions UF6 ↔ UF5 + F and UF6 ↔ UF4 + F2

Quantum-mechanical methods are used to assess the energy barriers to dissociation and recombination reactions of UF6 ↔ UF5 + F and UF6 ↔ UF4 + F2. The energy characteristics of these reactions are found to be strongly asymmetric: the dissociation reaction barriers exceed the recombination reactions barriers by more than 4 eV. The equilibrium atomic configurations of F2, UF4, UF5 and UF6 have been determined using precision quantum mechanical calculations. The U-F bond lengths obtained as a result of the calculations are in good agreement with experimental data. It was found that the decay reaction UF6 → UF5 + F is either barrier-free, or the energy barrier for such a reaction is less than the resolving power of the method (~ 0.1 eV). For the decay of UF6 → UF4 + F2, there is an energy barrier with a height of about 0.3 eV. An initial approximation was proposed for the arrangement of UF6 atoms in order to find the saddle points of the UF6 dissociation reactions. In this initial configuration, all 7 atoms of the UF6 molecule are located in the same plane. The F atoms are located at the vertices of a regular hexagon, and the U atom is at the center of such a hexagon. The results of this work can be used to determine the constants of thermal reactions of dissociation and recombination UF6 ↔ UF5 + F и UF6 ↔ UF4 + F2. These constants are necessary for modeling the physicochemical processes occurring during the enrichment of spent nuclear fuel (SNF).

The Xer activation factor of TLCΦ expands the possibilities for Xer recombination

ABSTRACTMany mobile elements take advantage of the highly-conserved chromosome dimer resolution system of bacteria, Xer. They participate in the transmission of antibiotic resistance and pathogenicity determinants. In particular, the toxin-linked cryptic satellite phage (TLCΦ) plays an essential role in the continuous emergence of new toxigenic clones of the Vibrio cholerae strain at the origin of the ongoing 7th cholera pandemic. The Xer machinery is composed of two chromosomally-encoded tyrosine recombinases, XerC and XerD. They resolve chromosome dimers by adding a crossover between sister copies of a specific 28 base pair site of bacterial chromosomes, dif. The activity of XerD depends on a direct contact with a cell division protein, FtsK, which spatially and temporally constrains the process. TLCΦ encodes for a XerD-activation factor (XafT), which drives the integration of the phage into the dif site of the primary chromosome of V. cholerae independently of FtsK. However, XerD does not bind to the attachment site (attP) of TLCΦ, which raised questions on the integration process. Here, we compared the integration efficiency of thousands of synthetic mini-TLCΦ plasmids harbouring different attP sites and assessed their stability in vivo. In addition, we compared the efficiency with which XafT and the XerD activation domain of FtsK drive recombination reactions in vitro. Taken together, our results suggest that XafT promotes the formation of synaptic complexes between canonical Xer recombination sites and imperfect sites.

Control of the serine integrase reaction: roles of the coiled-coil and helix E regions in DNA site synapsis and recombination

Bacteriophage serine integrases catalyze highly specific recombination reactions between defined DNA segments called att sites. These reactions are reversible depending upon the presence of a second phage-encoded directionality factor. The bipartite C-terminal DNA binding region of integrases includes a recombinase domain (RD) connected to a zinc-binding domain (ZD), which contains a long flexible coiled-coil (CC) motif that extends away from the bound DNA. We directly show that the identities of the phage A118 integrase att sites are specified by the DNA spacing between the RD and ZD DNA recognition determinants, which in turn, directs the relative trajectories of the CC motifs on each subunit of the att -bound integrase dimer. Recombination between compatible dimer-bound att sites requires minimal length CC motifs and 14 residues surrounding the tip where pairing of CC motifs between synapsing dimers occurs. Our alanine-scanning data suggests that molecular interactions between CC motif tips may differ in integrative ( attP x attB ) and excisive ( attL x attR ) recombination reactions. We identify mutations in 5 residues within the integrase oligomerization helix that control the remodeling of dimers into tetramers during synaptic complex formation. Whereas most of these gain-of-function mutants still require the CC motifs for synapsis, one mutant efficiently, but indiscriminantly, forms synaptic complexes without the CC motifs. However, the CC motifs are still required for recombination, suggesting a function for the CC motifs after initial assembly of the integrase synaptic tetramer. Importance The robust and exquisitely-regulated site-specific recombination reactions promoted by serine integrases are integral to the life cycle of temperate bacteriophage, and in the case of the A118 prophage, are an important virulence factor by Listeria monocytogenes . The properties of these recombinases have led to their repurposing into tools for genetic engineering and synthetic biology. In this report, we identify determinants regulating synaptic complex formation between correct DNA sites, including the DNA architecture responsible for specifying the identity of recombination sites, features of the unique coiled-coil structure on the integrase that are required to initiate synapsis, and amino acid residues on the integrase oligomerization helix that control the remodeling of synapsing dimers into a tetramer active for DNA strand exchange.

Archaeal tyrosine recombinases

ABSTRACT The integration of mobile genetic elements into their host chromosome influences the immediate fate of cellular organisms and gradually shapes their evolution. Site-specific recombinases catalyzing this integration have been extensively characterized both in bacteria and eukarya. More recently, a number of reports provided the in-depth characterization of archaeal tyrosine recombinases and highlighted new particular features not observed in the other two domains. In addition to being active in extreme environments, archaeal integrases catalyze reactions beyond site-specific recombination. Some of these integrases can catalyze low-sequence specificity recombination reactions with the same outcome as homologous recombination events generating deep rearrangements of their host genome. A large proportion of archaeal integrases are termed suicidal due to the presence of a specific recombination target within their own gene. The paradoxical maintenance of integrases that disrupt their gene upon integration implies novel mechanisms for their evolution. In this review, we assess the diversity of the archaeal tyrosine recombinases using a phylogenomic analysis based on an exhaustive similarity network. We outline the biochemical, ecological and evolutionary properties of these enzymes in the context of the families we identified and emphasize similarities and differences between archaeal recombinases and their bacterial and eukaryal counterparts.

Adaptive Response by an Electrolyte: Resilience to Electron Losses in a Dye-Sensitized Porous Photoanode

Photovoltage and photocurrents below theoretical limits in dye-sensitized photoelectrochemical solar energy conversion systems are usually attributed to electron loss processes such as dye-electron and electrolyte-electron recombination reactions within the porous...

LUMINESCENCE OF Α-WILLEMITE IN THE CATALYTIC OXIDATION OF CARBON MONOXIDE

The interaction of neutral gas particles of thermal energies (molecules and atoms) with the surface of a solid is accompanied by radiation in the visible and I.R. parts of the spectrum. In this case, the surface of a solid body acts as a catalyst for the recombination reactions of gas particles. In this connection, the possibility of exciting luminescence during the catalytic oxidation of carbon monoxide directly by the atomic form of oxygen pre-adsorbed on the surface of a solid is of interest. Kinetic and spectral methods were used to study the luminescence arising from the catalytic oxidation of carbon monoxide by the atomic form of oxygen preadsorbed on the surface of a solid – a sample of α-willemite Zn2SiO4:Mn2+. The main stages in the mechanisms of recombination between adsorbate particles are established. Electronic transitions in adsorption complexes and the activator ion have been identified. During the filling process, the sample temperature was maintained by a constant high-speed electronic control system of the heater current. This made it possible to avoid thermal side effects. The main stages in the mechanisms of recombination between adsorbate particles are established. Electronic transitions in adsorption complexes and the activator ion have been identified. It was found that luminescence excitation proceeds in two main stages, somewhat time-shifted. The two-stage mechanism for the catalytic oxidation of carbon monoxide on the surface of α-willemite with pre-adsorbed atomic oxygen allows a consistent description of the luminescence observed in this case. This type of luminescence has the prospect of using for studying the mechanisms of catalytic oxidation of carbon monoxide.

Measurement of NO_<i>x</i> and NO_<i>y</i> with a thermal dissociation cavity ring-down spectrometer (TD-CRDS): Instrument characterisation and first deployment

We present a newly constructed, two channel Thermal Dissociation Cavity Ring-Down Spectrometer (TD-CRDS) for the detection of NOx (NO + NO2), NOy (NOx + HNO3 + RO2NO2 + N2O5 etc.), NOz (NOy – NOx) and particulate nitrate (pNit). NOy-containing trace gases are detected as NO2 by CRDS at 405 nm following sampling through inlets at ambient temperature (NOx), or at 850 °C (NOy). In both cases, O3 was added to the air sample directly upstream of the cavities to convert NO (either ambient, or formed in the 850 °C oven) to NO2. An activated carbon denuder was used to remove gas-phase components of NOy when sampling pNit. Detection limits (1 minute averaging) for NOx, NOy and NOz are 98, 51 and 110 pptv, respectively. The total measurement uncertainties (at 50 % RH) in the NOx and NOy channels are 11 % + 10 pptv and 16 % + 14 pptv for NOz, respectively. Thermograms of various NOz species (peroxyacetyl nitrate, isopropyl nitrate, and HNO3) confirm stoichiometric conversion to NO2 (and/or NO) at the oven temperature and rule out significant interferences from NH3 detection or radical recombination reactions under ambient conditions. While fulfilling the requirement of high particle transmission and essentially complete removal of reactive nitrogen under dry conditions, the denuder suffered from NOx breakthrough and memory effects (i.e. release of stored NOy) under humid conditions. NOx measurements obtained from a ship sailing through the Red Sea, Indian Ocean and Arabian Gulf (NOx levels from