Synthesis of linear and tripoidal oligo(phenylene ethynylene)-based building blocks for application in modular DNA-programmed assembly

Rigid linear and tripoidal organic modules based on the oligo(phenylene ethynylene) backbone having salicylaldehyde-derived termini are synthesized. A highly functionalized 5-iodosalicyl aldehyde was prepared and coupled to each ethynyl group of 1,4-diethynylbenzene or 1,3,5-triethynylbenzene in Sonogashira couplings. The two or three termini of the compounds are functionalized for incorporation in linear and branched oligonucleotide strands. For the linear module (LM), the two termini are equipped with amide spacers, and one of these was functionalized with a DMTr (dimethoxytrityl)-protected hydroxy group and the other with a phosphoramidite. One of the tripoidal modules is prepared with DMTr groups in two of its three termini. A tripoidal module is also synthesized with three different groups on its hydroxy termini: a phosphoramidite, a DMTr group, and an Fmoc group. Extended studies have shown that these rigid linear and tripoidal organic modules can be incorporated into short oligonucleotides. Several of these modules can be applied for DNA-directed assembly and covalent coupling into structures of predetermined connectivity. Such structures have potential application for molecular electronics and nanotechnology.     

On the possible catalysis by single water molecules of gas-phase hydrogen abstraction reactions by OH radicals

The gas phase hydrogen abstraction reaction between OH and CY(2)XH, where X = H, F, OH, or NH(2) and Y = H, CH(3) or F, in the absence and presence of a single water molecule is investigated using both density function theory, B3LYP, and explicitly correlated coupled cluster theory, CCSD(T)-F12. We find that a single water molecule could have a catalytic effect at low temperatures possible in laboratory experiments, but does not seem to catalyze these reactions at 298 K, and will not play a role under relevant atmospheric conditions.     

Reductive Dephthalimidation: A Mild and Efficient Method for The N-Phthaumido Deprotection During Ougosaccharide Synthesis

Abstract

Synthesis of biologically active oligosaccharides, haptens and their protein conjugates is a major area of interest because of their role in antigen-antibody interaction and receptor effects¹. A number of these molecules contain α-or β-linked 2-acetamido-2-deoxy-D-glucosamine (GlcNAc) moieties. Most commonly, during the oligosaccharide synthesis, introduction of the β-glycosidically linked GlcNAc residue is achieved by either the oxazoline² or the phthalimido method³. Of these, the latter is preferred because 2-N-phthalimido protected glycosamine units having a halogen or a thioalkyl group at C-1 have consistently proved to be more efficient donors than are the oxazolines. However, time and again, subsequent conversion of the N-phthalimido to amine by hydrazinolysis has proved inadequate. This has often resulted in a poor overall yield after an otherwise efficient synthesis. Recently it was shown that the phthalimido function could be removed under mild conditions from a number of amino acids⁴. We now report that this technique can be efficiently used for the deprotection of the phthalimido function in suitably protected carbohydrate compounds (2,3 and 5).     

Synthesis of 2,6-Dideoxy-6-Thio Derivatives of KDO

ABSTRACT

Ammonium 2,3,6-trideoxy-2,6-epithio-D-manno-2-octenoate (8), ammonium 2,3,6-trideoxy-2,6-epithio-D-glycero-D-talo-octanoate (10a), ammonium 2,3,6-trideoxy-2,6-epithio-D-glycero-D-galacto-octanoate (10b) and ammonium 2,3,6-trideoxy-2,6-epithio-oxa-D-glycero-D-galacto-octanoate (13) have been synthesised as potential inhibitors of the enzyme CMP-KDO synthetase. The key step in the synthesis of 8 was the elimination of water from methyl 3,6-dideoxy-4,5:7,8-di-O-isopropylidene-6-thio-D-manno-2-octulosonate (4) using chlorodiphenylphosphine, imidazole and bromine to give the unsaturated methyl 2,3,6-trideoxy-2,6-epithio-4,5:7,8-di-O-isopropylidene-D-manno-2-octenoate (5). For the synthesis of 10a and 10b, zinc reduction of methyl 3,6-dideoxy-4,5:7,8-di-O-isopropylidene-6-S-(4-methoxybenzyl)-6-thio-2-O-(trichloro-tert-butoxycarbonyl)-D-manno-2-octenoate (2) gave an epimeric mixture of an α-hydroxyester 6 which was ring closed by in situ activation of the hydroxyl group using triphenylphosphine and tri-iodoimidazole followed by cleavage of the p-methoxybenzyl group to give 7a and 7b, which then were deprotected to give 10a and 10b.     

An Unusual Cyclic System: Derivatives of N-Acetyl [2-Deoxy-β-D-Mannopyranosid]Urono-6,2-Lactam

ABSTRACT

Syntheses are described of a new ring system, namely derivatives of N-acetyl [2-deoxy-β-D-mannopyranosid]urono-6,2-lactam. These were formed by participation of a 2-acetamido-2-deoxy group in the oxidation using pyridinium dichromate of a 6-hydroxyl group in a mannopyranosidic system The structures of the new compounds were determined mainly by NMR experiments inter alia by HMBC techniques.     

Single enzyme studies reveal the existence of discrete functional states for monomeric enzymes and how they are "selected" upon allosteric regulation

Allosteric regulation of enzymatic activity forms the basis for controlling a plethora of vital cellular processes. While the mechanism underlying regulation of multimeric enzymes is generally well understood and proposed to primarily operate via conformational selection, the mechanism underlying allosteric regulation of monomeric enzymes is poorly understood. Here we monitored for the first time allosteric regulation of enzymatic activity at the single molecule level. We measured single stochastic catalytic turnovers of a monomeric metabolic enzyme (Thermomyces lanuginosus Lipase) while titrating its proximity to a lipid membrane that acts as an allosteric effector. The single molecule measurements revealed the existence of discrete binary functional states that could not be identified in macroscopic measurements due to ensemble averaging. The discrete functional states correlate with the enzyme's major conformational states and are redistributed in the presence of the regulatory effector. Thus, our data support allosteric regulation of monomeric enzymes to operate via selection of preexisting functional states and not via induction of new ones.     

Bridging Ligand Length Controls AT Selectivity and Enantioselectivity of Binuclear Ruthenium Threading Intercalators

The slow dissociation of DNA threading intercalators makes them interesting as model compounds in the search for new DNA targeting drugs, as there appears to be a correlation between slow dissociation and biological activity. Thus, it would be of great value to understand the mechanisms controlling threading intercalation, and for this purpose we have investigated how the length of the bridging ligand of binuclear ruthenium threading intercalators affects their DNA binding properties. We have synthesised a new binuclear ruthenium threading intercalator with slower dissociation kinetics from ct‐DNA than has ever been observed for any ruthenium complex with any type of DNA, a property that we attribute to the increased distance between the ruthenium centres of the new complex. By comparison with previously studied ruthenium complexes, we further conclude that elongation of the bridging ligand reduces the sensitivity of the threading interaction to DNA flexibility, resulting in a decreased AT selectivity for the new complex. We also find that the length of the bridging ligand affects the enantioselectivity with increasing preference for the ΔΔ enantiomer as the bridging ligand becomes longer.     

Unexpected Isolation of 4‐Isothiocyanatomethylene‐4H‐pyridine‐1‐carboxylic Acid Ethyl Ester as Potential Template in Organic Synthesis

The synthesis of 4‐isothiocyanatomethyl‐pyridine 4 in 36% yield by Hasegawa and Kotani (Japanese patent 49088878, 1974) has spurred us to investigate this preparation in detail. In addition to this compound, 4‐isothiocyanatomethylene‐4H‐pyridine‐1‐carboxylic acid ethyl ester 3 can be isolated. The synthesis of both compounds 3 and 4 were optimized to 75% and 50% yield respectively. Reaction of compound 3 with methylamine gave thiourea derivatives 5, the same product obtained on reacting 4‐isothiocyanatomethyl‐pyridine 4 with methylamine. We succeed in adjusting the reaction conditions to obtain high yield either from compound 3 or isothiocyanate derivatives 4.