At Least n – 1 Intersection Points in a Connected Family of n Unit Circles in the Plane

Let C be a family of n different unit circles in the plane. We show that C determines at least n - c intersection points, where c is the number of connected components in ∪_{C ∈ C}C. This proves a conjecture of A. Bezdek.     

Highly efficient antibody-catalyzed deuteration of carbonyl compounds

Antibody 38C2 efficiently catalyzes deuterium-exchange reactions at the alpha position of a variety of ketones and aldehydes, including substrates that have a variety of sensitive functional groups. In addition to the regio- and chemoselectivity of these reactions, the catalytic rates (kcat) and rate-enhancement values (kcat/kun) are among the highest values ever observed with catalytic antibodies. Comparison of the substrate range of the catalytic antibody with highly evolved aldolase enzymes, such as rabbit-muscle aldolase, highlights the much broader practical scope of the antibody, which accepts a wide range of substrates. The hydrogen-exchange reaction was used for calibration and mapping of the antibody active site. Isotope-exchange experiments with cycloheptanone reveal that the formation of the Schiff base species (as concluded from the 16O/18O exchange rate at the carbonyl oxygen) is much faster than the formation of the enamine intermediate (as concluded from the H/D exchange rate), and both steps are faster than the antibody-catalyzed aldol addition reaction.     

A versatile toolbox for variable DNA functionalization at high density

To broaden the applicability of chemically modified DNAs in nano- and biotechnology, material science, sensor development, and molecular recognition, strategies are required for introducing a large variety of different modifications into the same nucleic acid sequence at once. Here, we investigate the scope and limits for obtaining functionalized dsDNA by primer extension and PCR, using a broad variety of chemically modified deoxynucleotide triphosphates (dNTPs), DNA polymerases, and templates. All natural nucleobases in each strand were substituted with up to four different base-modified analogues. We studied the sequence dependence of enzymatic amplification to yield high-density functionalized DNA (fDNA) from modified dNTPs, and of fDNA templates, and found that GC-rich sequences are amplified with decreased efficiency as compared to AT-rich ones. There is also a strong dependence on the polymerase used. While family A polymerases generally performed poorly on "demanding" templates containing consecutive stretches of a particular base, family B polymerases were better suited for this purpose, in particular Pwo and Vent (exo-) DNA polymerase. A systematic analysis of fDNAs modified at increasing densities by CD spectroscopy revealed that single modified bases do not alter the overall B-type DNA structure, regardless of their chemical nature. A density of three modified bases induces conformational changes in the double helix, reflected by an inversion of the CD spectra. Our study provides a basis for establishing a generally applicable toolbox of enzymes, templates, and monomers for generating high-density functionalized DNAs for a broad range of applications.     

Aerobic Iron‐Based Cross‐Dehydrogenative Coupling Enables Efficient Diversity‐Oriented Synthesis of Coumestrol‐Based Selective Estrogen Receptor Modulators

An iron‐based cross‐dehydrogenative coupling (CDC) approach was applied for the diversity‐oriented synthesis of coumestrol‐based selective estrogen receptor modulators (SERMs), representing the first application of CDC chemistry in natural product synthesis. The first stage of the two‐step synthesis of coumestrol involved a modified aerobic oxidative cross‐coupling between ethyl 2‐(2,4‐dimethoxybenzoyl)acetate and 3‐methoxyphenol, with FeCl₃ (10 mol %) as the catalyst. The benzofuran coupling product was then subjected to sequential deprotection and lactonization steps, affording the natural product in 59 % overall yield. Based on this new methodology other coumestrol analogues were prepared, and their effects on the proliferation of the estrogen receptor (ER)‐dependent MCF‐7 and of the ER‐independent MDA‐MB‐231 breast cancer cells were tested. As a result, new types of estrogen receptor ligands having an acetamide group instead of the 9‐hydroxyl group of coumestrol were discovered. Both 9‐acetamido‐coumestrol and 8‐acetamidocoumestrol were found more active than the natural product against estrogen‐dependent MCF‐7 breast cancer cells, with IC₅₀ values of 30 and 9 nM , respectively.     

Erratum to: Preserving the activity of enzymes under harsh oxidizing conditions: sol–gel entrapped alkaline phosphatase exposed to bromine

Chemically reactive sol–gel matrices hold the ability of protecting entrapped enzymes from destruction by external harsh chemicals. We show this concept by exposing alkaline phosphatase (AlP) to a strong oxidizing agent—bromine. In solution, AlP is immediately destroyed by this oxidant. When AlP was entrapped in hybrid silica sol–gel materials carrying double bonds, the reactivity of AlP was preserved after exposure to bromine under conditions which totally destroy it in solution. The matrices studied were vinylated and allylated silicas, and their protectability was compared to n-alkylated silicas and to silica itself. For instance, the reactivity of AlP entrapped in allylated silica after exposure to 25.6 mM bromine solution is 40 times higher than its reactivity when entrapped in pure silica; and in solution the enzyme is totally destroyed at this concentration. Molecular level mechanisms for these observations are proposed.     

Structural elucidation of V‐type nerve agents by liquid chromatography/electrospray ionization mass spectrometry

V‐nerve agents present information‐poor spectra, both in GC‐EI‐MS and LC‐ESI‐MS/MS, with dominant fragments/product ions corresponding to the amine‐containing residue. Hence, derivatives/isomers with the same amine residue exhibit similar mass spectral patterns, leading to ambiguity in the phosphonate structure. We present a simple approach for their structural elucidation based on two complementary experiments: ESI‐MS/MS of the original compound, which provides information about the amine moiety, and ESI‐MS/MS of the phosphonic acid hydrolysis products generated by N‐iodosuccinimide, which provides ions' characteristic of the phosphonate structure. This approach enables the structural elucidation of the original V‐agents with a higher degree of certainty.     

Ferrioxamine B analogues: targeting the FoxA uptake system in the pathogenic Yersinia enterocolitica

A series of ferrioxamine B analogues that target the bacterium Yersinia enterocolitica were prepared. These iron carriers are composed of three hydroxamate-containing monomeric units. Two identical monomers consist of N-hydroxy-3-aminopropionic acid coupled with beta-alanine, and a third unit at the amino terminal is composed of N-hydroxy-3-aminopropionic acid and one of the following amino acids: beta-alanine (1a), phenylalanine (1b), cyclohexylalanine (1c), or glycine (1d). Thermodynamic results for representatives of the analogues have shown a strong destabilization (3-4 orders of magnitude) of the ferric complexes with respect to ferrioxamine B, probably due to shorter spacers and a more strained structure around the metal center. No significant effect of the variations at the N-terminal has been observed on the stability of the ferric complexes. By contrast, using in vivo radioactive uptake experiments, we have found that these modifications have a substantial effect on the mechanism of iron(III) uptake in the pathogenic bacteria Yersinia enterocolitica. Analogues 1a and 1d were utilized by the ferrioxamine B uptake system (FoxA), while 1b and 1c either used different uptake systems or were transported to the microbial cell nonspecifically by diffusion via the cell membrane. Transport via the FoxA system was also confirmed by uptake experiments with the FoxA deficient strain of Yersinia enterocolitica. A fluorescent marker, attached to 1a in a way that did not interfere with its biological activity, provided additional means to monitor the uptake mechanism by fluorescence techniques. Of particular interest is the observation that 1a was utilized by the uptake system of ferrioxamine B in Yersinia enterocolitica (FoxA) but failed to use the ferrioxamine uptake route in Pseudomonas putida. Here, we present a case in which biomimetic siderophore analogues deliberately designed for a particular bacterium can distinguish between related uptake systems of different microorganisms.     

Sol-gel materials as efficient enzyme protectors: preserving the activity of phosphatases under extreme ph conditions

By entrapment in (surfactant modified) silica sol-gel matrixes, alkaline phosphatase (AlP) -- naturally with optimum activity at pH 9.5 -- was kept functioning at extreme acidic environments as low as pH 0.9, and acid phosphatase (AcP) -- naturally with optimum activity at pH 4.5 -- was kept functioning at extreme alkaline environments, up to pH 13.0. Propositions are offered as to the origin of the ability of the matrixes to provide such highly efficient protection and as to the origin of the synergetic enhancing effect when both the silica and the surfactants are used as a combined entrapping environment. It was found that the protectability of the enzymes against harsh pH values is dependent on the nature of the surfactant.