New Method for Synthesis of Methacrylate-Type Polymerizable Ionic Liquids

A new method for the synthesis of polymerizable ionic liquids bearing a methacrylate moiety was developed with the aim to avoid premature polymerization of synthesized compounds. Spacer length between the imidazolium cation and the polymerizable functional group varied from 2 to 10 carbon atoms. Different 1-(n-hydroxyalkyl)-3-methylimidazolium bromides and 1-[n-(methacryloyloxy)-alkyl]-3-methylimidazolium bromides were obtained with very good yields (more than 90%).

[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource: Full experimental and spectral details.]     

DNA curtains and nanoscale curtain rods: high-throughput tools for single molecule imaging

Single molecule visualization of protein-DNA complexes can reveal details of reaction mechanisms and macromolecular dynamics inaccessible to traditional biochemical assays. However, these techniques are often limited by the inherent difficulty of collecting statistically relevant information from experiments explicitly designed to look at single events. New approaches that increase throughput capacity of single molecule methods have the potential for making these techniques more readily applicable to a variety of biological questions involving different types of DNA transactions. Here we show that nanofabricated chromium barriers, which are located at strategic positions on a fused silica slide otherwise coated with a supported lipid bilayer, can be used to organize DNA molecules into molecular curtains. The DNA that makes up the curtains is visualized by total internal reflection fluorescence microscopy (TIRFM) allowing simultaneous imaging of hundreds or thousands of aligned molecules. These DNA curtains present a robust experimental platform portending massively parallel data acquisition of individual protein-DNA interactions in real time.     

Fully automated chip‐based negative mode nanoelectrospray mass spectrometry of fructooligosaccharides produced by heterologously expressed levansucrase from Pseudomonassyringae pv. tomato DC3000

Pseudomonas syringae pathovars possess multiple levansucrases with still unclear specific roles for bacteria. We have cloned and expressed three levansucrase genes, lsc1, lsc2 and lsc3, from P. syringae DC3000 in Escherichia coli. Levansucrases synthesize a high molecular weight fructan polymer, levan, from sucrose and in the case of some levansucrases, fructooligosaccharides (FOS) with potential prebiotic effects are also produced. The ability of purified Lsc3 protein of DC3000 to synthesize FOS was tested using prolonged incubation time and varied concentrations of sugar substrates. Thin‐layer chromatography (TLC) analysis of reaction products disclosed formation of FOS from both sucrose and raffinose, revealing a new catalytic property for P. syringae levansucrases. In order to analyze Lsc3‐produced FOS in underivatized form, we optimized a novel method recently introduced in carbohydrate research, based on fully automated chip‐based nanoelectrospray ionization (nanoESI) high‐capacity ion trap mass spectrometry (HCT‐MS). Uding chip‐based nanoESI MS in negative ion mode, FOS, with degrees of polymerization up to five, were detected in reaction mixtures of Lsc3 with sucrose and raffinose. For confirmation, further structural analysis by tandem mass spectrometry (MS/MS) employing collision‐induced dissociation at low energies was performed. To validate the method, commercial inulin‐derived FOS preparations Orafti®P95 and Orafti®Synergy1, which are currently used as prebiotics, were used as controls. By chip‐based nanoESI HCT‐MS, similar FOS distribution was observed in these reference mixtures. Thereby, the obtained data allowed us to postulate that FOS produced by the Lsc3 protein of P. syringae DC3000 may be prebiotic as well. Copyright © 2009 John Wiley & Sons, Ltd.     

Parallel arrays of geometric nanowells for assembling curtains of DNA with controlled lateral dispersion

The analysis of individual molecules is evolving into an important tool for biological research, and presents conceptually new ways of approaching experimental design strategies. However, more robust methods are required if these technologies are to be made broadly available to the biological research community. To help achieve this goal we have combined nanofabrication techniques with single-molecule optical microscopy for assembling and visualizing curtains comprised of thousands of individual DNA molecules organized at engineered diffusion barriers on a lipid bilayer-coated surface. Here we present an important extension of this technology that implements geometric barrier patterns comprised of thousands of nanoscale wells that can be loaded with single molecules of DNA. We show that these geometric nanowells can be used to precisely control the lateral distribution of the individual DNA molecules within curtains assembled along the edges of the engineered barrier patterns. The individual molecules making up the DNA curtain can be separated from one another by a user-defined distance dictated by the dimensions of the nanowells. We demonstrate the broader utility of these patterned DNA curtains in a novel, real time restriction assay that we refer to as dynamic optical restriction mapping, which can be used to rapidly identify entire sets of cleavage sites within a large DNA molecule.