Deuterium-labelled N-acyl-L-homoserine lactones (AHLs)--inter-kingdom signalling molecules--synthesis, structural studies, and interactions with model lipid membranes

N-Acyl-l-homoserine lactones (AHLs) are synthesized by Gram-negative bacteria. These quorum-sensing molecules play an important role in the context of bacterial infection and biofilm formation. They also allow communication between microorganisms and eukaryotic cells (inter-kingdom signalling). However, very little is known about the entire mechanism of those interactions. Precise structural studies are required to analyse the different AHL isomers as only one form is biologically most active. Theoretical studies combined with experimental infrared and Raman spectroscopic data are therefore undertaken to characterise the obtained compounds. To mimic interactions between AHL and cell membranes, we studied the insertion of AHL in supported lipid bilayers, using vibrational sum-frequency-generation spectroscopy. Deuterium-labelled AHLs were thus synthesized. Starting from readily available deuterated fatty acids, a two-step procedure towards deuterated N-acyl-l-homoserine lactones with varying chain lengths is described. This included the acylation of Meldrum’s acid followed by amidation. Additionally, the detailed analytical evaluation of the products is presented herein.     

Preparation,Characterization and Electromagnetic Shielding Effectiveness of Conductive Polythiophene/Poly(ethylene terephthalate) Composite Fibers

Conductive polythiophene (PTh)/poly(ethylene terephthalate) (PET) composite fibers were prepared by polymerization of thiophene in the presence of PET fibers in acetonitrile medium using FeCl₃. The effects of polymerization conditions such as oxidant/monomer mol ratio and polymerization temperature and time on PTh content and surface electrical resistivity of PTh/PET composite fiber were investigated in detail. It was observed that the usage of preswelled PET fibers in dichloromethane increased the PTh content and decreased surface resistivity of composite fiber. Composite fiber having the highest PTh content (5.7%) and the lowest surface resistivity (80 kΩ) was obtained at 20°C with 1.25 M FeCl₃ and 0.42 M thiophene concentrations. The washing effects of laundering detergent and dry cleaning liquid on surface resistivity of composite fibers were investigated. The electromagnetic shielding effectiveness (EMSE) and relative shielding efficiency by absorption and reflection of composite fibers were measured in the radio and microwave frequency range. The results show that the EMSE values decreased with increasing frequency from radio waves to microwaves with an attenuation of 21 dB to 4 dB.     

Novel Copolymers of Styrene and Alkoxy Ring‐Substituted 2‐Cyano‐N,N‐Dimethyl‐3‐Phenyl‐2‐Propenamides

Electrophilic trisubstituted ethylene monomers, alkoxy ring‐substituted 2‐cyano‐N,N‐dimethyl‐3‐phenyl‐2‐propenamides, RC₆H₄CH?C(CN)CON(CH₃)₂ (where R is 2‐OCH₃, 3‐OCH₃, 4‐OCH₃, 2‐OCH₂CH₃, 3‐OCH₂CH₃, 4‐OCH₂CH₂CH₃, 4‐OCH₂CH₂CH₂CH₃), were synthesized by potassium hydroxide catalyzed Knoevenagel condensation of ring‐substituted benzaldehydes and N,N‐dimethyl cyanoacetamide, and characterized by CHN elemental analysis, IR, ¹H‐ and ¹³C‐NMR. Novel copolymers of the ethylenes and styrene were prepared at equimolar monomer feed composition by solution copolymerization in the presence of a radical initiator, ACBN at 70°C. The composition of the copolymers was calculated from nitrogen analysis, and the structures were analyzed by IR, ¹H and ¹³C NMR, GPC, DSC, and TGA. High T_g of the copolymers in comparison with that of polystyrene indicates a substantial decrease in chain mobility of the copolymer due to the high dipolar character of the trisubstituted ethylene monomer unit. The gravimetric analysis indicated that the copolymers decompose in the 300–450°C range.     

Poly(acrylate‐b‐styrene‐b‐isobutylene‐b‐styrene‐b‐acrylate) Block Copolymers via Carbocationic and Atom Transfer Radical Polymerizations

A series of polyacrylate‐polystyrene‐polyisobutylene‐polystyrene‐polyacrylate (X‐PS‐PIB‐PS‐X) pentablock terpolymers (X=poly(methyl acrylate) (PMA), poly(butyl acrylate) (PBA), or poly(methyl methacrylate) (PMMA)) was prepared from poly (styrene‐b‐isobutylene‐b‐styrene) (PS‐PIB‐PS) block copolymers (BCPs) using either a Cu(I)Cl/1,1,4,7,7‐pentamethyldiethylenetriamine (PMDETA) or Cu(I)Cl/tris[2‐(dimethylamino)ethyl]amine (Me₆TREN) catalyst system. The PS‐PIB‐PS BCPs were prepared by quasiliving carbocationic polymerization of isobutylene using a difunctional initiator, followed by the sequential addition of styrene, and were used as macroinitiators for the atom transfer radical polymerization (ATRP) of methyl acrylate (MA), n‐butyl acrylate (BA), or methyl methacrylate (MMA). The ATRP of MA and BA proceeded in a controlled fashion using either a Cu(I)Cl/PMDETA or Cu(I)Cl/Me₆TREN catalyst system, as evidenced by a linear increase in molecular weight with conversion and low PDIs. The polymerization of MMA was less controlled. ¹H‐NMR spectroscopy was used to elucidate pentablock copolymer structure and composition. The thermal stabilities of the pentablock copolymers were slightly less than the PS‐PIB‐PS macroinitiators due to the presence of polyacrylate or polymethacrylate outer block segments. DSC analysis of the pentablock copolymers showed a plurality of glass transition temperatures, indicating a phase separated material.     

ASSESSMENT OF GENOTOXICITY AND MUTAGENICITY OF 1,2-DIOXETANES IN HUMAN CELLS USING A PLASMID SHUTTLE VECTOR

Abstract— 1,2-Dioxetanes are efficient sources of triplet excited carbonyl compounds on thermal decomposition. They cause photochemical and photobiological transformations in the dark. In order to study the genotoxicity and mutagenicity of 1,2-dioxetanes, the replicating shuttle vector pZ189 was damaged with 3,3,4-trimethyl-l,2-dioxetane(TrMD) or 3-hydroxymethyl-3,4,4-trimethyl-l,2-dioxetane (HTMD) in vitro and subsequently transfected into normal human lymphoblasts. We found a dose-dependent increase of genotoxicity (decrease of plasmid survival) and increase of mutation frequency with both dioxetanes. However, TrMD was less mutagenic than HTMD at similar genotoxicity. Sequence analysis of the supF gene revealed more point mutations than deletions. Single base substitutions occurred exclusively at G:C sites: 94.6% of point mutations with TrMD and 100% with HTMD were G:C to T:A and G:C to C:G transversions. These are the typical mutations following 7,8-dihydro-8-oxoguanine (8-oxo-G) formation, the main DNA lesion induced by TrMD and HTMD. Only with TrMD we found 5.4% G:C to A:T transitions, probably reflecting the more pronounced ability of TrMD to form some pyrimidine dimers. Our results indicate that 8-oxo-G is also the most relevant modification in in vivo mutagenesis.     

In situ Synthesis of Oligonucleotide Arrays on Surfaces Coated with Crosslinked Polymer Multilayers

We report an approach to the in situ synthesis of oligonucleotide arrays on surfaces coated with crosslinked polymer multilayers. Our approach makes use of methods for the 'reactive' layer-by-layer assembly of thin, amine-reactive multilayers using branched polyethyleneimine (PEI) and the azlactone-functionalized polymer poly(2-vinyl-4,4'-dimethylazlactone) (PVDMA). Post-fabrication treatment of film-coated glass substrates with d-glucamine or 4-amino-1-butanol yielded hydroxyl-functionalized films suitable for the Maskless Array Synthesis (MAS) of oligonucleotide arrays. Glucamine-functionalized films yielded arrays of oligonucleotides with fluorescence intensities and signal-to-noise ratios (after hybridization with fluorescently labeled complementary strands) comparable to those of arrays fabricated on conventional silanized glass substrates. These arrays could be exposed to multiple hybridization-dehybridization cycles with only moderate loss of hybridization density. The versatility of the layer-by-layer approach also permitted synthesis directly on thin sheets of film-coated poly(ethylene terephthalate) (PET) to yield flexible oligonucleotide arrays that could be readily manipulated (e.g., bent) and cut into smaller arrays. To our knowledge, this work presents the first use of polymer multilayers as a substrate for the multi-step synthesis of complex molecules. Our results demonstrate that these films are robust and able to withstand the ~450 individual chemical processing steps associated with MAS (as well as manipulations required to hybridize, image, and dehybridize the arrays) without large-scale cracking, peeling, or delamination of the thin films. The combination of layer-by-layer assembly and MAS provides a means of fabricating functional oligonucleotide arrays on a range of different materials and substrates. This approach may also prove useful for the fabrication of supports for the solid-phase synthesis and screening of other macromolecular or small-molecule agents.     

Investigation of reactions postulated to occur during inhibition of ribonucleotide reductases by 2'-azido-2'-deoxynucleotides

Model 3'-azido-3'-deoxynucleosides with thiol or vicinal dithiol substituents at C2' or C5' were synthesized to study reactions postulated to occur during inhibition of ribonucleotide reductases by 2'-azido-2'-deoxynucleotides. Esterification of 5'-(tert-butyldiphenylsilyl)-3'-azido-3'-deoxyadenosine and 3'-azido-3'-deoxythymidine (AZT) with 2,3-S-isopropylidene-2,3-dimercaptopropanoic acid or N-Boc-S-trityl-L-cysteine and deprotection gave 3'-azido-3'-deoxy-2'-O-(2,3-dimercaptopropanoyl or cysteinyl)adenosine and the 3'-azido-3'-deoxy-5'-O-(2,3-dimercaptopropanoyl or cysteinyl)thymidine analogs. Density functional calculations predicted that intramolecular reactions between generated thiyl radicals and an azido group on such model compounds would be exothermic by 33.6-41.2 kcal/mol and have low energy barriers of 10.4-13.5 kcal/mol. Reduction of the azido group occurred to give 3'-amino-3'-deoxythymidine, which was postulated to occur with thiyl radicals generated by treatment of 3'-azido-3'-deoxy-5'-O-(2,3-dimercaptopropanoyl)thymidine with 2,2'-azobis-(2-methyl-2-propionamidine) dihydrochloride. Gamma radiolysis of N(2)O-saturated aqueous solutions of AZT and cysteine produced 3'-amino-3'-deoxythymidine and thymine most likely by both radical and ionic processes.     

RNA encapsidation by SV40-derived nanoparticles follows a rapid two-state mechanism

Remarkably, uniform virus-like particles self-assemble in a process that appears to follow a rapid kinetic mechanism. The mechanisms by which spherical viruses assemble from hundreds of capsid proteins around nucleic acid, however, are yet unresolved. Using time-resolved small-angle X-ray scattering (TR-SAXS), we have been able to directly visualize SV40 VP1 pentamers encapsidating short RNA molecules (500mers). This assembly process yields T = 1 icosahedral particles comprised of 12 pentamers and one RNA molecule. The reaction is nearly one-third complete within 35 ms, following a two-state kinetic process with no detectable intermediates. Theoretical analysis of kinetics, using a master equation, shows that the assembly process nucleates at the RNA and continues by a cascade of elongation reactions in which one VP1 pentamer is added at a time, with a rate of approximately 10(9) M(-1) s(-1). The reaction is highly robust and faster than the predicted diffusion limit. The emerging molecular mechanism, which appears to be general to viruses that assemble around nucleic acids, implicates long-ranged electrostatic interactions. The model proposes that the growing nucleo-protein complex acts as an electrostatic antenna that attracts other capsid subunits for the encapsidation process.     

Unexpected consequences of block polydispersity on the self-assembly of ABA triblock copolymers

Controlled/"living" polymerizations and tandem polymerization methodologies offer enticing opportunities to enchain a wide variety of monomers into new, functional block copolymer materials with unusual physical properties. However, the use of these synthetic methods often introduces nontrivial molecular weight polydispersities, a type of chain length heterogeneity, into one or more of the copolymer blocks. While the self-assembly behavior of monodisperse AB diblock and ABA triblock copolymers is both experimentally and theoretically well understood, the effects of broadening the copolymer molecular weight distribution on block copolymer phase behavior are less well-explored. We report the melt-phase self-assembly behavior of SBS triblock copolymers (S = poly(styrene) and B = poly(1,4-butadiene)) comprised of a broad polydispersity B block (M(w)/M(n) = 1.73-2.00) flanked by relatively narrow dispersity S blocks (M(w)/M(n) = 1.09-1.36), in order to identify the effects of chain length heterogeneity on block copolymer self-assembly. Based on synchrotron small-angle X-ray scattering and transmission electron microscopy analyses of seventeen SBS triblock copolymers with poly(1,4-butadiene) volume fractions 0.27 ≤ f(B) ≤ 0.82, we demonstrate that polydisperse SBS triblock copolymers self-assemble into periodic structures with unexpectedly enhanced stabilities that greatly exceed those of equivalent monodisperse copolymers. The unprecedented stabilities of these polydisperse microphase separated melts are discussed in the context of a complete morphology diagram for this system, which demonstrates that narrow dispersity copolymers are not required for periodic nanoscale assembly.     

In silico mutagenesis and docking study of Ralstonia solanacearum RSL lectin: performance of docking software to predict saccharide binding

In this study, in silico mutagenesis and docking in Ralstonia solanacearum lectin (RSL) were carried out, and the ability of several docking software programs to calculate binding affinity was evaluated. In silico mutation of six amino acid residues (Agr17, Glu28, Gly39, Ala40, Trp76, and Trp81) was done, and a total of 114 in silico mutants of RSL were docked with Me-α-L-fucoside. Our results show that polar residues Arg17 and Glu28, as well as nonpolar amino acids Trp76 and Trp81, are crucial for binding. Gly39 may also influence ligand binding because any mutations at this position lead to a change in the binding pocket shape. The Ala40 residue was found to be the most interesting residue for mutagenesis and can affect the selectivity and/or affinity. In general, the docking software used performs better for high affinity binders and fails to place the binding affinities in the correct order.