Electron microscopy studies on DNA recognition by DNA-PK

Advances in transmission electron microscopy coupled to increasingly powerful biocomputing techniques are opening enormous possibilities to understand the structure and function of complex biological processes performed by large multi-protein assemblies. This is an exciting time for electron microscopists because we can combine our efforts with X-ray crystallographers and NMR spectroscopists to reach the prospect of studying the structure and dynamics of the so-called ‘molecular machines’. One of these fascinating systems is the macromolecular complex formed around double-stranded DNA breaks (DSBs). Non-homologous end-joining (NHEJ) is the main DSBs repair pathway in mammalian cells, where a collection of proteins interact to rejoin two broken DNA ends. During NHEJ, DNA-dependent protein kinase (DNA-PK) binds damaged DNA with high affinity and acts as the main scaffold for other repair factors. Several studies have made use of the electron microscope to reveal the three-dimensional architecture of DNA-PK and the structural basis for the recognition of damaged DNA and the activation of DNA-PK's kinase activity.     

Three-component Ugi-Smiles couplings of cyclic imines

Cyclic imines react with isocyanides and electron-deficient phenols to afford N-aryl piperidines and pyrrolidines in good yields (Ugi-Smiles couplings of cyclic imines). The starting imines were formed by oxidation with N-chlorosuccinimide followed by a base-induced dehydrochlorination.     

Intramolecular Alkynylogous Mukaiyama Aldol Reaction Starting from Bicyclic Alkanones Tethered to Alkynyl Esters: Formal Total Synthesis of (±)‐Hamigeran B

Selecting the ring : tert‐Butyldimethylsilyltriflate (TBSOTf)/NEt₃ treatment of alkynyl esters tethered to bicycloalkanones leads to the formation of tricyclic allenoates with total diasteroselectivity at the ring junction. An intramolecular alkynylogous Mukaiyama aldol reaction promoted by a TBSOTf/NEt₃ dual activation is involved. This novel methodology was illustrated by a formal total synthesis of (±)‐hamigeran B.

     

Determination of the helical screw sense and side-group chirality of a synthetic chiral polymer from Raman optical activity

Splitting it up: Excellent agreement between the experimental and the quantum-chemically simulated Raman optical activity (ROA) spectrum of (+)-poly(trityl methacrylate) shows that the polymer backbone adopts a left-handed helical conformation while the trityl side groups display a left-handed propeller conformation. Thus ROA can be used to determine the complete structure of synthetic chiral polymers in solution.     

Application of multiresolution analyses to electron density maps of small molecules: Critical point representations for molecular superposition

Three different methods are applied to generate low resolution molecular electron density (ED) distribution functions: a crystallography-based formalism, an analytical approach which allows the calculation of a promolecular ED distribution in terms of a weighted summation over atomic ED distributions, and a wavelet-based multiresolution analysis approach. Critical point graph representations of the molecular ED distributions are then generated by locating points where the gradient of the density is equal to zero, and further considered for pairwise molecular superpositions of thrombin inhibitors using a Monte Carlo/Simulated Annealing technique.     

N-3 alkylation of uracils with unprotected amino alcohols using the Mitsunobu reaction

During our search for novel CGRP antagonists, we had great difficulty in accessing one of our key motifs. Herein, we communicate how we solved the problem by an unprecedented Mitsunobu alkylation using unprotected amino alcohols.     

Frequency-Dependent Streaming Potentials

An experimental apparatus and data acquisition system was constructed to measure the streaming potential coupling coefficients as a function of frequency. The purpose of the experiments was to measure, for the first time, the real and imaginary portion of streaming potentials. In addition, the measured frequency range was extended beyond any previous measurements. Frequency-dependent streaming potential experiments were conducted on one glass capillary and two porous glass filters. The sample pore diameters ranged from 1 mm to 34 μm. Two frequency-dependent models (Packard and Pride) were compared to the data. Both Pride's and Packard's models have a good fit to the experimental data in the low- and intermediate-frequency regime. In the high-frequency regime, the data fit the theory after being corrected for capacitance effects of the experimental setup. Pride's generalized model appears to have the ability to more accurately estimate pore sizes in the porous medium samples. Packard's model has one unknown model parameter while Pride's model has four unknown model parameters, two of which can be independently determined experimentally. Pride's additional parameters may allow for a determination of permeability. Copyright 2001 Academic Press.