Alteration in the choice of DNA repair pathway with increasing sequence selective DNA alkylation in the minor groove

BACKGROUND: Many conventional DNA alkylating anticancer drugs form adducts in the major groove of DNA. These are known to be chiefly repaired by both nucleotide (NER) and base (BER) excision repair in eukaryotic cells. Much less is known about the repair pathways acting on sequence specific minor groove purine adducts, which result from a promising new class of anti-tumour agents. RESULTS: Benzoic acid mustards (BAMs) tethering 1-3 pyrrole units (compounds 1, 2 and 3) show increasing DNA sequence selectivity for alkylation from BAM and 1, alkylating primarily at guanine-N7 in the major groove, to 3 which is selective for alkylation in the minor groove at purine-N3 in the sequence 5'-TTTTGPu (Pu=guanine or adenine). This increasing sequence selectivity is reflected in increased toxicity in human cells. In the yeast Saccharomyces cerevisiae, the repair of untargeted DNA adducts produced by BAM, 1 and 2 depends upon both the NER and BER pathways. In contrast, the repair of the sequence specific minor groove adducts of 3 does not involve known BER or NER activities. In addition, neither recombination nor mismatch repair are involved. Two disruptants from the RAD6 mutagenesis defective epistasis group (rad6 and rad18), however, showed increased sensitivity to 3. In particular, the rad18 mutant was over three orders of magnitude more sensitive to 3 compared to its isogenic parent, and 3 was highly mutagenic in the absence of RAD18. Elimination of the sequence specific DNA adducts formed by 3 was observed in the wild type strain, but these lesions persisted in the rad18 mutant. CONCLUSIONS: We have demonstrated that the repair of DNA adducts produced by the highly sequence specific minor groove alkylating agent 3 involves an error free adduct elimination pathway dependent on the Rad18 protein. This represents the first systematic analysis of the cellular pathways which modulate sensitivity to this new class of DNA sequence specific drugs, and indicates that the enhanced cytotoxicity of certain sequence specific minor groove adducts in DNA is the result of evasion of the common excision repair pathways.     

Configuration biased Monte Carlo and Brownian dynamics simulations of semiflexible polymers in extensional flows

Configuration Biased Monte Carlo (CBMC) and Non-Equilibrium Brownian Dynamics (NEBD) simulations are used to understand the dynamics of semi-flexible macromolecules undergoing extensional flow. The mathematical model utilizes a discretized version of the Kratky-Porod wormlike (or persistent) chain as the building block, and using kinetic theory, generalized to include flow. In steady, potential flows, the solution of the Fokker-Planck equation exists and is used in the generation of trial and acceptance moves in the CBMC scheme. For the NEBD, the Fokker-Planck equation is converted to a Stochastic Differential Equation (SDE) from which the simulation algorithm is obtained. Various conformational quantities are monitored, under both steady-state and transient conditions, with the primary independent variable being the flexibility parameter β, the bending constant of the chain. It is found that the model is able to describe qualitatively many of the experimentally observed effects in such systems. In particular, we find that there is a direct link between the molecular flexibility and its birefringence response in an elongational flow field. We are able to draw conclusions by considering the behavior of molecular-conformational quantities such as the radius of gyration and the moment of inertia.     

Properties of Single-Component Metal–Organic Framework Crystal-Glass Composites

The formation, and subsequent structural, thermal and adsorptive properties of single-component metal–organic framework crystal-glass composites (MOF-CGCs) are investigated. A series of novel materials exhibiting chemically identical glassy and crystalline phases within the same material were produced, where crystalline ZIF-62(Zn) was incorporated within an a_gZIF-62(Zn) matrix. X-ray diffraction showed that the crystalline phase was still present after heating to above the glass transition temperature of a_gZIF-62(Zn), and interfacial compatibility between the crystalline and glassy phases was investigated using a mixed-metal (ZIF-62(Co))_0.5(a_gZIF-62(Zn))_0.5 analogue. CO₂ gas adsorption measurements showed that the CO₂ uptakes of the MOF-CGCs were between those of the crystalline and glassy phases.     

Continuous and pulsed ultrasound-assisted extractions of antioxidants from pomegranate peel

There is a great demand for developing efficient extraction methods in order to reduce extraction time and increase the yield and activity of functional antioxidants. The yields, activities, and extraction kinetics of antioxidants from the dry peel of pomegranate marc were studied using ultrasound-assisted extraction in continuous and pulsed modes and the results were compared with conventional extraction (CE) at a temperature of 25 ± 2 °C and water/peel ratio of 50/1, w/w. The studied factors were intensity level and treatment time for continuous ultrasound-assisted extraction (CUAE), and intensity level, number of pulse repetition, and pulse duration and interval for pulsed ultrasound-assisted extraction (PUAE). The results showed that all factors significantly affected the antioxidant yield, but only treatment time had a significant effect on the antioxidant activity. Compared to CE, PUAE at an intensity level of 59.2 W/cm², and a pulse duration of 5 s and a resting interval of 5 s increased the antioxidant yield by 22% and reduced the extraction time by 87%. Similarly, CUAE at the same intensity level increased the antioxidant yield by 24% and reduced the extraction time by 90%. Since PUAE had 50% energy saving compared to CUAE, we recommend using PUAE for the extraction with antioxidant yield of 14.5% and DPPH scavenging activity of 5.8 g/g. A second-order kinetic model was successfully developed for describing the mechanism of ultrasound-assisted extractions under PUAE and CUAE. This research clearly demonstrated the superiority of PUAE for producing antioxidants from peel of pomegranate marc.     

A fully implicit direct Newton's method for the steady-state Navier–Stokes equations

Newton's method and banded Gaussian elimination can be a CPU efficient method for steady-state solutions to two-dimensional Navier–Stokes equations. In this paper we look at techniques that increase the radius of convergence of Newton's method, reduce the number of times the Jacobian must be factored, and simplify evaluation of the Jacobian. The driven cavity and natural convection problems are used as test problems, and finite volume discretization is employed.