Differential rates of reversibility of ecteinascidin 743-DNA covalent adducts from different sequences lead to migration to favored bonding sites.

Ecteinascidin 743 (Et 743), one of a series of structurally related antitumor antibiotics isolated from a marine tunicate, is currently in phase II clinical trials. Et 743 alkylates guanine N2 through the minor groove of DNA. Hydrogen-bonding networks that associate the drug with a three base pair DNA recognition site have been proposed to contribute to both the reactivity and the stability of the Et 743-DNA adduct. Here, we report that the reaction of Et 743 with DNA is reversible under nondenaturing conditions and that the rate of this reverse reaction depends critically upon the DNA-modified sequence. Quite unexpectedly, it was found that although the rates of alkylation are similar for the 5'-AGT and 5'-AGC sequences, reversal from the 5'-AGT sequence occurs faster than from the 5'-AGC sequence. Consequently, it is the differences in the rate of the reverse reaction that dictate the sequence selectivity of Et 743 toward its favored target sequence. As a direct consequence of the reversible nature of Et 743 with DNA, Et 743 can migrate from the nonfavored bonding sequence (e.g., 5'-AGT) to the favored DNA target site (e.g., 5'-AGC). The data suggest that the observed differences in the rate of reversibility arise from differences in the stability of the Et 743-DNA adduct at the 5'-AGT and 5'-AGC target sequences. On the basis of gel electrophoresis and (1)H NMR experiments, the Et 743-AGT adduct is less stable, has more dynamic motion, and produces different conformational changes in the DNA than the more stable Et 743-AGC adduct. The shuffling of Et 743-DNA adducts to the more stable alkylation sites has important implications for understanding the underlying relationship between the structural modification of DNA by Et 743 and its biological potency and efficacy in tumor cells.     

Eulerian tour algorithms for data visualization and the PairViz package

PairViz is an R package that produces orderings of statistical objects for visualization purposes. We abstract the ordering problem to one of constructing edge-traversals of (possibly weighted) graphs. PairViz implements various edge traversal algorithms which are based on Eulerian tours and Hamiltonian decompositions. We describe these algorithms, their PairViz implementation and discuss their properties and performance. We illustrate their application to two visualization problems, that of assessing rater agreement, and model comparison in regression.     

Graphs as navigational infrastructure for high dimensional data spaces

We propose using graph theoretic results to develop an infrastructure that tracks movement from a display of one set of variables to another. The illustrative example throughout is the real-time morphing of one scatterplot into another. Hurley and Oldford (J Comput Graph Stat 2010) made extensive use of the graph having variables as nodes and edges indicating a paired relationship between them. The present paper introduces several new graphs derivable from this one whose traversals can be described as particular movements through high dimensional spaces. These are connected to known results in graph theory and the graph theoretic results applied to the problem of visualizing high-dimensional data.     

Molecular structure and IR absorption spectra of perfluorinated aldehyde hydrates (n-CxF2x+1CH(OH)2, x = 1-4)

Structures and IR absorption spectra of the conformational isomers of perfluorinated aldehyde hydrates, n-C_xF_2x+1CH(OH)₂, (x = 1-4) have been calculated using density functional theory (DFT) and compared to experimental FT-IR measurements. Two absorption peaks around 3600-3700 cm⁻¹ were observed and are assigned to OH stretching modes of OH groups with, and without, intramolecular hydrogen bonding. For n-C₃F₇CH(OH)₂, two absorption bands around 900-1000 cm⁻¹ were observed in the experimental spectra, whereas only a single in-phase stretching mode of the (CF₃)(C₂F₄CH(OH)₂) and (C₃F₇)(CH(OH)₂) bonds was calculated for each conformer. The experimental spectra were well described by composite spectra of the thermal equilibrium mixture of different conformational isomers of n-C_xF_2x+1CH(OH)₂ calculated by DFT.     

Enhanced selectivities for the hydroxyl-directed methanolysis of esters using the 2-acyl-4-aminopyridine class of acyl transfer catalysts: ketones as binding sites

In this paper we describe the preparation of a series of 2-acyl-4-aminopyridines, and their use as catalysts for the hydroxyl-directed methanolysis of alpha-hydroxy esters in preference to alpha-methoxy esters. Hydroxyl-direction with these catalysts, which contain ketones at the 2-position of the pyridine, is achieved by reversible addition of the alcohol of the hydroxy ester to the ketone to provide the corresponding hemiketal. Their activity is compared to that of the previously described catalyst 2-formyl-4-pyrrolidinopyridine (FPP), which contains an aldehyde at the 2-position of the pyridine. The catalysts which contain ketones at the 2-position range in reactivity from 10 times slower to slightly faster than FPP, and certain of these are much more selective for the methanolysis of hydroxy esters than FPP. This increase in selectivity is ascribed to a decrease in the rate of the nondirected methanolysis reaction with the ketone-derived catalysts. The evidence suggests that the nondirected reaction does not proceed by an intermolecular general base mechanism, but rather via a nucleophilic catalysis mechanism in which the hydroxyl group of the hemiacetal formed upon addition of methanol to the aldehyde of FPP acts as the nucleophile. Since the hydroxyl group derived from a hemiketal is more hindered and less nucleophilic than that derived from a hemiacetal, the nondirected reaction is much slower for the catalysts containing ketones as binding sites.     

Rapid cloning and expression of a fungal polyketide synthase gene involved in squalestatin biosynthesis

PCR primers designed to selectively amplify the unique C-methyltransferase domain of fungal polyketide synthases were used to selectively clone a polyketide synthase gene involved in the biosynthesis of the squalene synthase inhibitor squalestatin S1 , heterologous expression of which led to the biosynthesis of the squalestatin side-chain.     

$\mathfrak{D}$ -Differentiation in Hilbert Space and the Structure of Quantum Mechanics

An appropriate kind of curved Hilbert space is developed in such a manner that it admits operators of - and -differentiation, which are the analogues of the familiar covariant and D-differentiation available in a manifold. These tools are then employed to shed light on the space-time structure of Quantum Mechanics, from the points of view of the Feynman ‘path integral’ and of canonical quantisation. (The latter contains, as a special case, quantisation in arbitrary curvilinear coordinates when space is flat.) The influence of curvature is emphasised throughout, with an illustration provided by the Aharonov-Bohm effect.