Noncovalent DNA binding drives DNA alkylation by leinamycin: evidence that the Z,E-5-(thiazol-4-yl)-penta-2,4-dienone moiety of the natural product serves as an atypical DNA intercalator

Molecular recognition and chemical modification of DNA are important in medicinal chemistry, toxicology, and biotechnology. Historically, natural products have revealed many interesting and unexpected mechanisms for noncovalent DNA binding and covalent DNA modification. The studies reported here characterize the molecular mechanisms underlying the efficient alkylation of duplex DNA by the Streptomyces-derived natural product leinamycin. Previous studies suggested that alkylation of duplex DNA by activated leinamycin (2) is driven by noncovalent association of the natural product with the double helix. This is striking because leinamycin does not contain a classical noncovalent DNA-binding motif, such as an intercalating unit, a groove binder, or a polycation. The experiments described here provide evidence that leinamycin is an atypical DNA-intercalating agent. A competition binding assay involving daunomycin-mediated inhibition of DNA alkylation by leinamycin provided evidence that activated leinamycin binds to duplex DNA with an apparent binding constant of approximately 4.3 ± 0.4 × 10(3) M(-1). Activated leinamycin caused duplex unwinding and hydrodynamic changes in DNA-containing solutions that are indicative of DNA intercalation. Characterization of the reaction of activated leinamycin with palindromic duplexes containing 5'-CG and 5'-GC target sites, bulge-containing duplexes, and 5-methylcytosine-containing duplexes provided evidence regarding the orientation of leinamycin with respect to target guanine residues. The data allow construction of a model for the leinamycin-DNA complex suggesting how a modest DNA-binding constant combines with proper positioning of the natural product to drive efficient alkylation of guanine residues in the major groove of duplex DNA.     

A reconstructed discontinuous Galerkin method for multi-material hydrodynamics with sharp interfaces

Discontinuous Galerkin (DG) methods have been well established for single-material hydrodynamics. However, consistent DG discretizations for non-equilibrium multi-material (more than two materials) hydrodynamics have not been extensively studied. In this work, a novel reconstructed DG (rDG) method for the single-velocity multi-material system is presented. The multi-material system being considered assumes stiff velocity relaxation, but does not assume pressure and temperature equilibrium between the multiple materials. A second-order DG(P₁) method and a third-order least-squares based rDG(P₁P₂) are used to discretize this system in space, and a third-order total variation diminishing (TVD) Runge-Kutta method is used to integrate in time. A well-balanced DG discretization of the non-conservative system is presented and is verified by numerical test problems. Furthermore, a consistent interface treatment is implemented, which ensures strict conservation of material masses and total energy. Numerical tests indicate that the DG and rDG methods are, indeed, the second- and third-order accurate. Comparisons with the second-order finite volume method show that the DG and rDG methods are able to capture the interfaces more sharply. The DG and rDG methods are also more accurate in the single-material regions of the flow. This work focuses on the general multidimensional rDG formulation of the non-equilibrium multi-material system and a study of properties of the method via one-dimensional numerical experiments. The results from this research will be the foundation for a multidimensional high-order rDG method for multi-material hydrodynamics.     

Tensor product representation of qubit and its transform under linear-operator action

The general one-particle spin states are considered. It is shown that information contained in a spin-1/2 state can be recorded in an equivalent form with the help of three mixed completely decoherent qubit states. The density matrix of such a system has the form of the tensor product of three diagonal matrices. The linear operator defined in the space of one-particle spin states generates some transform of the tensor products of the diagonal matrices. We construct this transform in the explicit form.     

Features of the hedritic morphology of β‐isotactic polypropylene studied by atomic force microscopy

The lamellar organization of melt‐crystallized β‐isotactic polypropylene was studied by atomic force microscopy (AFM) after permanganic etching. Hedritic objects grown at a high crystallization temperature (140–143 °C) were investigated. Essential features of the hedritic development were revealed by the characteristic projections exposed at the sample surface. A three‐dimensional view of the morphology was obtained by AFM. Hedritic growth proceeded mainly by branching around screw dislocations resulting in new lamellae that further developed. Successive lamellar layers often diverged. Deviation from the planar lamellar habit was observed, varying with the position within the hedrite. Twisting of the lamellae also was observed occasionally in the vicinity of the screw dislocations. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 672–681, 2000     

Stimuli‐responsive antifouling polyisobutylene‐based biomaterials via modular surface functionalization

This article demonstrates a new, modular approach to surface functionalization that harnesses chain entanglement. A layer of functionalized polyisobutylene, (PIB)‐ω, where ω = ‐OH, ‐thymine (T), ‐hexaethylene glycol (HEG), poly(ethylene glycol) (‐PEG‐OH), methoxy‐functionalized poly(ethylene glycol) (‐PEG‐OCH₃), and ‐tetraethylene glycol‐α‐lipoate (TEG‐αL) was adhered to PIB‐based thermoplastic elastomer (TPE) surfaces. X‐ray photoelectron spectroscopy (XPS) at angles ranging from 20° to 75° showed decreasing polar group concentration with increasing penetration depth, confirming segregation of polar groups toward the surface. Water contact angle (WCA) of the PIB‐based TPE dropped from 95° to 79°?83° upon coating, and soaking in water for 24 h further decreased the WCA. Dynamic WCA measurements showed 40–30° receding angles, showing that stimulus from an aqueous environment elicits enrichment of polar groups on the surface. Fibrinogen (Fg) adsorption on the various surfaces was quantified using surface plasmon resonance (SPR). Static and dynamic WCA did not vary significantly among TPE + PIB‐ω surfaces, but there were dramatic differences in Fg adsorption: 256 ng/cm² was measured on the native TPE, which dropped to 40 and 22 ng/cm² on PIB‐PEG‐OCH₃ and PIB‐PEG‐OH‐coated surfaces. PIB‐TEG‐αL‐coated surfaces presented the lowest Fg adsorption with 14 ng/cm². © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55 , 1742–1749     

Optimization of Plant Sample Preparation and ICP Parameters for Analysis of Phosphorus

Abstract

Parameters of HNO₃-H₂O₂ wet digestion sample preparation method and inductively coupled plasma atomic emission spectrometer