Uracil-DNA glycosylase efficiency is modulated by substrate rigidity.

Uracil DNA-glycosylase (UNG) is a DNA repair enzyme that removes the highly mutagenic uracil lesion from DNA using a base flipping mechanism. Although this enzyme has evolved to remove uracil from diverse sequence contexts, UNG excision efficiency depends on DNA sequence. To provide the molecular basis for rationalizing UNG substrate preferences, we used time-resolved fluorescence spectroscopy, NMR imino proton exchange measurements, and molecular dynamics simulations to measure UNG specificity constants (kcat/KM) and DNA flexibilities for DNA substrates containing central AUT, TUA, AUA, and TUT motifs. Our study shows that UNG efficiency is dictated by the intrinsic deformability around the lesion, establishes a direct relationship between substrate flexibility modes and UNG efficiency, and shows that bases immediately adjacent to the uracil are allosterically coupled and have the greatest impact on substrate flexibility and UNG activity. The finding that substrate flexibility controls UNG efficiency is likely significant for other repair enzymes and has major implications for the understanding of mutation hotspot genesis, molecular evolution, and base editing.

Synthesis, Postsynthetic Modifications, and Applications of the First Quinoxaline-Based Covalent Organic Framework.

We report a new synthetic protocol for preparing highly ordered two-dimensional nanoporous covalent organic frameworks (2D-COFs) based on a quinoxaline backbone. The quinoxaline framework represents a new type of COF that enables postsynthetic modification by placing two different chemical functionalities within the nanopores including layer-to-layer cross-linking. We also demonstrate that membranes fabricated using this new 2D-COF perform highly selective separations resulting in dramatic performance enhancement post cross-linking.

Proton Transfer and Ionicity: An 15N NMR Study of Pyridine Base Protonation.

Protic ionic liquids (PILs) are made by proton transfer from a Brønsted acid to a base and are of interest for their solvent and electrolyte properties such as high ionic conductivity. Unfortunately, many PILs have been misnamed, because their ionic content is minimal due to an insufficient driving force for the proton transfer. Here we review this problem and introduce a new method, using 15N NMR spectroscopy, of characterizing the relation between the extent of proton transfer to a given base and the strength of the proton-donating acid. The experimental data reveal a sigmoid "titration type" curve that indicates clearly the acid strength, at which molecule bases, of substituted pyridine type, are fully protonated. We compare results for two bases of similar shape but different basicity, protonated by equimolar amounts of the different acids. The extent of protonation is also reflected in the ionic conductivity, and we show that the important part of the protonation sigmoid is quantitatively reproduced by data for conductivity and viscosity displayed in the form of a Walden plot (log equivalent conductivity vs log fluidity). The acid strength, for this study, is based on gas phase proton affinities, but we note that a similar sigmoid is obtained if we use the condensed phase Hammett acidity functions instead. Our findings allow us to rank the AlCl4- anion as the weakest proton acceptor in use in IL studies, consistent with its role in the most conductive ILs.

Hierarchical spidroin micellar nanoparticles as the fundamental precursors of spider silks.

Many natural silks produced by spiders and insects are unique materials in their exceptional toughness and tensile strength, while being lightweight and biodegradable-properties that are currently unparalleled in synthetic materials. Myriad approaches have been attempted to prepare artificial silks from recombinant spider silk spidroins but have each failed to achieve the advantageous properties of the natural material. This is because of an incomplete understanding of the in vivo spidroin-to-fiber spinning process and, particularly, because of a lack of knowledge of the true morphological nature of spidroin nanostructures in the precursor dope solution and the mechanisms by which these nanostructures transform into micrometer-scale silk fibers. Herein we determine the physical form of the natural spidroin precursor nanostructures stored within spider glands that seed the formation of their silks and reveal the fundamental structural transformations that occur during the initial stages of extrusion en route to fiber formation. Using a combination of solution phase diffusion NMR and cryogenic transmission electron microscopy (cryo-TEM), we reveal direct evidence that the concentrated spidroin proteins are stored in the silk glands of black widow spiders as complex, hierarchical nanoassemblies (∼300 nm diameter) that are composed of micellar subdomains, substructures that themselves are engaged in the initial nanoscale transformations that occur in response to shear. We find that the established micelle theory of silk fiber precursor storage is incomplete and that the first steps toward liquid crystalline organization during silk spinning involve the fibrillization of nanoscale hierarchical micelle subdomains.

NMR Characterization of Ionicity and Transport Properties for a Series of Diethylmethylamine Based Protic Ionic Liquids.

The ionicity and transport properties of a series of diethylmethylamine (DEMA) based protic ionic liquids (PILs) were characterized, principally utilizing nuclear magnetic resonance (NMR) spectroscopy. PILs were formed via the protonation of DEMA by an array of acids spanning a large range of acidities. A correlation between the (1)H chemical shift of the exchangeable proton and the acidity of the acid used for the synthesis of the PIL was observed. The gas phase proton affinity of the acid was found to be a better predictor of the extent of proton transfer than the commonly used aqueous ΔpKa. Pulsed field gradient (PFG) NMR was used to determine the diffusivity of the exchangeable proton in a subset of the PILs. The exchangeable proton diffuses with the acid if the PIL is synthesized with a weak acid, and with the base if a strong acid is used. The ionicity of the PILs was characterized using the Walden analysis and by comparing to the ideal Nernst-Einstein conductivity predicted from the (1)H PFG-NMR results.

Phase progression of γ-Al2O3 nanoparticles synthesized in a solvent-deficient environment.

Our simple and uniquely cost-effective solvent-deficient synthetic method produces 3-5 nm Al2O3 nanoparticles which show promise as improved industrial catalyst-supports. While catalytic applications are sensitive to the details of the atomic structure, a diffraction analysis of alumina nanoparticles is challenging because of extreme size/microstrain-related peak broadening and the similarity of the diffraction patterns of various transitional Al2O3 phases. Here, we employ a combination of X-ray pair-distribution function (PDF) and Rietveld methods, together with solid-state NMR and thermogravimetry/differential thermal analysis-mass spectrometry (TG/DTA-MS), to characterize the alumina phase-progression in our nanoparticles as a function of calcination temperature between 300 and 1200 °C. In the solvent-deficient synthetic environment, a boehmite precursor phase forms which transitions to γ-Al2O3 at an extraordinarily low temperature (below 300 °C), but this γ-Al2O3 is initially riddled with boehmite-like stacking-fault defects that steadily disappear during calcination in the range from 300 to 950 °C. The healing of these defects accounts for many of the most interesting and widely reported properties of the γ-phase.

Determining the equation of state of amorphous solids at high pressure using optical microscopy.

A method to determine the volumetric equation of state of amorphous solids using optical microscopy in a diamond anvil cell is described. The method relies on two- dimensional image acquisition and analysis to quantify changes in the projected image area with compression. The area analysis methods prove to be robust against improper focusing and lighting conditions while providing the accuracy necessary to deduce small area changes, which correspond to small volume changes in an isotropic material. The image capture, area analysis method is used to determine the compression of cubic crystals, yielding results in good agreement with diffraction and volumetric measurements. As a proof of concept, the equation of state of amorphous red phosphorus is measured up to 12 GPa under hydrostatic conditions where the quantified volume change between the red and black phases is approximately ΔV/V(0) ≈ 0.05 after a reduction of volume nearing 35% at 8 GPa. A large hysteresis is present during decompression and eventually results in a 15% permanent densification relative to the starting volume, which is attributed to a pressure induced crystallization from red to black phosphorus. The robustness of the technique is also demonstrated by measuring the equation of state of GeSe(2) glasses for semi transparent samples and As(2)O(3) in which gold coating is used as a contrasting aid.