3′-Oligonucleotides conjugation via chemoselective oxime bond formation

Chemoselective oxime ligation of cyclopeptide, fluorescein and mannose derivatives at the 3′-end of an oligonucleotide was achieved. The conjugation was performed by reacting oxyamine containing reporter groups to an oligonucleotide bearing an aldehyde at the 3′-extremity. The aldehyde was generated by mild periodate oxidation of a 1,2-aminoalcohol which was readily incorporated at the 3′-end by automated DNA synthesis using the corresponding commercially available support. The straightforward chemical access, their stability in biological media as well as their unchanged hybridisation properties emphasise the interest of such 3′-conjugates.     

Versatile synthesis of head group functionalized phospholipids via oxime bond formation

A method for introduction of various head groups on phospholipid frameworks via oxime bond formation has been developed for the synthesis of cyclen-Cu(II), pyrene, naphthalene, and other headgroup functionalized phospholipids that can cleave the membrane protein, hemagglutinin.     

Internalization of a peptide into multilamellar vesicles assisted by the formation of an alpha-oxo oxime bond

As part of a drug-delivery project, we designed and synthesised a novel hydroxylamine cholesterol-based anchor to ensure the chemoselective ligation of recognition patterns onto multilamellar vesicles by oxime ligation. The entry of a glyoxylyl peptide into the vesicles was unexpectedly assisted by the formation of the alpha-oxo oxime bond. We studied extensively the kinetic and thermodynamic aspects of this phenomenon. Briefly, for a glyoxylyl peptide, the speed and ability to enter the vesicle were dependent upon 1) the presence of a hydroxylamine anchor of the type CholE3ONH2, 2) the amount of peptide engaged in the ligation and 3) the flip-flop motion permitted by the different formulations, in which the presence of cholesterol seems to play an important role.     

Aldehyde detection by chromogenic/fluorogenic oxime bond fragmentation

Amination of 4-nitrophenol, umbelliferone and 4-methylumbelliferone gave the corresponding oxyamines 1-3. These oxyamines react with aldehydes and ketones to form oximes. In the case of aliphatic aldehydes and electron-poor aromatic aldehydes, the oximes undergo base-catalyzed fragmentation in aqueous buffer in the presence of bovine serum albumin to give the parent phenols, which is the acyclic analog of Kemp's elimination reaction of 5-nitrobenzisoxazole 28. The process can be used as a spectrophotometric assay for formaldehyde under aqueous neutral conditions.     

The oxime bond formation as a useful tool for the preparation of oligonucleotide conjugates

Synthetic oligonucleotides are attracting considerable interest as potential therapeutic agents for the selective inhibition of gene expression. The attainment of effective cellular delivery however remains a problem. The conjugation of oligonucleotides to cell penetrating peptides is one of the most promising alternatives, that is being currently investigated to improve the uptake efficiency of oligonucleotides. The synthesis of peptide–oligonucleotide conjugates (POC) is however still a problem. Work from our laboratory has attempted to address the problem of POC synthesis by using the chemoselective oxime bond formation. Herein, we present an account of the work accomplished in our laboratory in the recent past, concerning the conjugation of various reporters to oligonucleotides. To cite this article: Y. Singh et al., C. R. Chimie 8 (2005).     

New solid support for the synthesis of 3'-oligonucleotide conjugates through glyoxylic oxime bond formation

A novel solid support 1 was synthesized to incorporate glyoxylic aldehyde functionality at the oligonucleotide 3'-terminus. 6-mer and 11-mer oligonucleotide sequences containing 3'-glyoxylic aldehyde functionality were prepared by using this support. These modified oligonucleotides were coupled to reporters containing an aminooxy group to prepare oligonucleotide 3'-conjugates through glyoxylic oxime bond formation. The hydrolytic stability of a glyoxylic oxime linkage was also investigated. [reaction: see text].     

Iterative oxime bond chemistry leads to protease inhibitors

[structure: see text] In the present paper, we have looked at iterative coupling as a strategy to form new druglike molecules. We have developed an iterative coupling chemistry based on oxime bond formation between hydroxyaromatic aldehyde building blocks to form linear oxime oligomers. The strategy is validated by the discovery of micromolar protease inhibitors.     

The oxime bond formation as an efficient tool for the conjugation of ruthenium complexes to oligonucleotides and peptides

A convenient method for the conjugation of ruthenium complex on oligonucleotides and peptides through chemoselective oxime linkage is reported. Novel Ru(II) complexes sustaining an aminooxy containing ligand were prepared and efficiently coupled with the oligonucleotides and peptides functionalized with the complementary reactive aldehyde group. The method described herein could be a useful tool for preparing a broad range of metal complex-oligonucleotide and peptide conjugates.     

Peptidomimetic bond formation by DNA-templated acyl transfer

The efficiencies of DNA-templated acyl transfer reactions between a thioester modified oligonucleotide and a series of amine and thiol based nucleophiles are directly compared. The reactivity of the nucleophile, reaction conditions (solvent, buffer, pH) and linker length all play important roles in determining the efficiency of the transfer reaction. Careful optimisation of the system enables the use of DNA-templated synthesis to form stable peptide-like bonds under mild aqueous conditions close to neutral pH.     

Shape-shifting micro- and nanopatterns controlled by temperature

Herein, features that alter their shape to form a different pattern upon an external trigger are described. Electron-beam lithography was used to fabricate micrometer- and nanometer-sized surface immobilized poly(triethylene glycol methacrylate) (pTEGMA) that exhibits significant thermal responsivity; the resulting hydrogels collapsed by up to 95% of their height upon addition of heat. Multicomponent features composed of both the thermoresponsive polymer and nonresponsive poly(ethylene glycol) (PEG) were then prepared. Upon increase in temperature, only the thermally responsive component of the pattern collapsed, causing a significant and predictable alteration in the overall pattern. Reversible micrometer- and nanometer-sized square-to-triangles, squares-to-checkerboards, smiles-to-neutral face, and zeros-to-ones shapes were shown.     

Phosphorus-carbon bond formation catalysed by electrophilic N-heterocyclic phosphines

A P-chloro-diazaphospholene catalyses the phosphorus-carbon bond formation reaction between diphenylsilylphosphine and various alkyl chlorides.     

Fast carbon-carbon bond formation by a promiscuous lipase

Lipase B from Candida antarctica was redesigned to catalyze the promiscuous reaction of carbon-carbon bond formation. Mutation of the catalytic serine to alanine afforded a mutant that catalyzed Michael additions of 1,3-dicarbonyls to alpha,beta-unsaturated carbonyl compounds at high specific rates, such as 4000 s-1. The enzyme-catalyzed Michael addition reaction followed saturation kinetics and showed substrate inhibition. The designed enzyme showed high rate enhancements with a catalytic proficiency higher than 108, which is on the same level as that observed for enzymes with native substrates.     

A molecular orbital explanation of bond distance variation caused by hydrogen bond formation

For hydrogen bond systems X–D–HA–Y, a simple molecular orbital model is proposed to understand the mechanism of the bond distance variations caused by the hydrogen bond formation. This model explains the bond distance variations for X–D and A–Y as follows. Electrostatic potential that the electrons in a molecule receive from other molecules causes the changes in atomic orbital energy differences between the bonded atoms. Then, the changes in the orbital energy differences make the bond orders larger or smaller and consequently the bond distances vary. The validity of this model has been confirmed by the effective fragment potential method, using the test systems of (HCOOH)₂, HCONH₂ (formamide) crystal and BF₃·2H₂O crystal.     

Cobalt-catalyzed aryl-sulfur bond formation

A new cobalt-catalyzed coupling of aryl halides with thiophenols and alkanethiols is reported. A variety of aryl sulfides can be prepared in excellent yields under mild reaction conditions using 1-2 mol % of CoI2(dppe) and Zn. This new cobalt-catalyzed coupling represents an interesting addition to previously known methods to synthesize thioethers. [reaction: see text].     

Hydrogen bond network formation

The signs of the dynamic dichroism of the NH stretch and the amide I bands in nylons were found to be counterintuitive. Experiments show that polymer chains tend to align in the direction of an applied tensile strain. The CH stretching bands in nylons exhibit the expected negative dynamic dichroism indicating chain alignment in the strain direction. The ΔA′ peaks for the NH and amide I bands are positive. The ΔA′ peak for the NH band is also unusual in that it has a derivative shape. This can be explained by band shifts brought about by anisotropic changes in the intermolecular spacing in the glassy polymer. Above T_g the derivative shape disappears but the ΔA′ peak for both the NH and amide I absorption remain positive. We postulate that the positive ΔA′ peaks of the NH and amide I bands result from a hydrogen bonding network where stress is transmitted through a network consisting of covalent chains connected by hydrogen bonds.     

Polymerization of diacetylenes by hydrogen bond templated adlayer formation

Adlayers were formed on self-assembled monolayers (SAMs) formed by alkanethiols on gold. Base SAMs exposing amide functional groups at the SAM surface were formed with 12-mercaptododecanamide. Adlayers of diacetylene-containing monomers were then formed via amide hydrogen bonding in decalin and decalin/toluene mixtures. Grazing angle FTIR, contact angle measurements, and ellipsometry suggest that these adlayer films exhibit ordering and packing similar to that of SAMs on gold. Resonance Raman spectroscopy showed that these diacetylene adlayers could be readily polymerized by exposure to UV light.