Convertible and Constrained Nucleotides: The 2'-Deoxyribose 5'-C-Functionalization Approach, a French Touch.

Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5'-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson-Crick base-pairing.

Convertible and conformationally constrained nucleic acids (CNAs).

We introduce the concept of Convertible and Constrained Nucleic Acids (CNAs). By means of the synthesis of a stereocontrolled N-propargyl dioxo-1,3,2-oxaza-phosphorinane as an internucleotidic linkage, the torsional angles α and β can adopt either the canonical (g, t) set of values able to increase DNA duplex stability or the non-canonical (g, t) set that stabilized the hairpin structure when installed within the loop moiety. With an appended propargyl function on the nitrogen atom of the six-membered ring, the copper catalysed Huisgen's cycloaddition (CuAAC click chemistry) allows for the introduction of new functionalities at any location on the nucleic acid chain while maintaining the properties brought by the geometrical constraint and the neutral internucleotidic linkage.

DNA Three Way Junction Core Decorated with Amino Acids-Like Residues-Synthesis and Characterization.

Construction and physico-chemical behavior of DNA three way junction (3WJ) functionalized by protein-like residues (imidazole, alcohol and carboxylic acid) at unpaired positions at the core is described. One 5'-C(S)-propargyl-thymidine nucleotide was specifically incorporated on each strand to react through a post synthetic CuACC reaction with either protected imidazolyl-, hydroxyl- or carboxyl-azide. Structural impacts of 5'-C(S)-functionalization were investigated to evaluate how 3WJ flexibility/stability is affected.

Differential effects on allele selective silencing of mutant huntingtin by two stereoisomers of α,β-constrained nucleic acid.

We describe the effects of introducing two epimers of neutral backbone α,β-constrained nucleic acid (CNA) on the activity and allele selectivity profile of RNase H active antisense oligonucleotides (ASOs) targeting a single nucleotide polymorphism (SNP) for the treatment of Huntington's disease (HD). ASOs modified with both isomers of α,β-CNA in the gap region showed good activity versus the mutant allele, but one isomer showed improved selectivity versus the wild-type allele. Analysis of the human RNase H cleavage patterns of α,β-CNA modified ASOs versus matched and mismatched RNA revealed that both isomers support RNase H cleavage on the RNA strand across from the site of incorporation in the ASO--an unusual observation for a neutral linkage oligonucleotide modification.

Structure binding relationship of galactosylated Glycoclusters toward Pseudomonas aeruginosa lectin LecA using a DNA-based carbohydrate microarray.

Pseudomonas aeruginosa (PA) is a major public health issue due to its impact on nosocomial infections as well as its impact on cystic fibrosis patient mortality. One of the main concerns is its ability to develop antibiotic resistance. Therefore, inhibition of PA virulence has been proposed as an alternative strategy to tackle PA based infections.

Prebiotically plausible oligoribonucleotide ligation facilitated by chemoselective acetylation.

The recent synthesis of pyrimidine ribonucleoside-2',3'-cyclic phosphates under prebiotically plausible conditions has strengthened the case for the involvement of ribonucleic acid (RNA) at an early stage in the origin of life. However, a prebiotic conversion of these weakly activated monomers, and their purine counterparts, to the 3',5'-linked RNA polymers of extant biochemistry has been lacking (previous attempts led only to short oligomers with mixed linkages). Here we show that the 2'-hydroxyl group of oligoribonucleotide-3'-phosphates can be chemoselectively acetylated in water under prebiotically credible conditions, which allows rapid and efficient template-directed ligation.

Synthesis of homo- and heterofunctionalized glycoclusters and binding to Pseudomonas aeruginosa lectins PA-IL and PA-IIL.

Homo- and heterofunctionalized glycoclusters with galactose and/or fucose residues targeting both PA-IL and PA-IIL lectins of Pseudomonas aeruginosa were synthesized using "Click" chemistry and DNA chemistry. Their binding to lectins (separately or in a mixture) was studied using a DNA Directed Immobilization carbohydrate microarray. Homoglycoclusters bind selectively to their lectin while the heteroglycocluster binds simultaneously both lectins with a slight lower affinity.

Synthesis of a library of fucosylated glycoclusters and determination of their binding toward Pseudomonas aeruginosa lectin B (PA-IIL) using a DNA-based carbohydrate microarray.

Pseudomonas aeruginosa (PA) is a Gram negative opportunistic pathogen and is the major pathogen encounter in the cystic fibrosis (CF) lung airways. It often leads to chronic respiratory infection despite aggressive antibiotic therapy due to the emergence of resistant strains and to the formation of biofilm. The lectin PA-IIL (LecB) is a fucose-specific lectin from PA suspected to be involved in host recognition/adhesion and in biofilm formation.

Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions.

At some stage in the origin of life, an informational polymer must have arisen by purely chemical means. According to one version of the 'RNA world' hypothesis this polymer was RNA, but attempts to provide experimental support for this have failed. In particular, although there has been some success demonstrating that 'activated' ribonucleotides can polymerize to form RNA, it is far from obvious how such ribonucleotides could have formed from their constituent parts (ribose and nucleobases).

Anti-retroviral and cytostatic activity of 2',3'-dideoxyribonucleoside 3'-disulfides.

Herein, we report the synthesis, antiviral and cytostatic effects of nucleosides bearing a 3'-disulfide function as prodrugs of potentially active 3'-mercaptonucleotides. The lack of the anti-HIV effects in mutant CEM/TK-cells for most of the thymidine disulfides suggests that a phosphorylation step involving thymidine kinase is necessary for the eventual antiviral activity of the thymidine nucleosides. The comparable anti-HIV activities of most of the disulfides and their rapid reduction in CEM cell extracts imply an inhibitory effect of the 2',3'-dideoxy-3'-mercaptothymidine 5'-triphosphate metabolite.

Direct preparation of nucleoside vinyl disulfides from 2-(trimethylsilyl)ethyl sulfides, an access to vinylthiols.

We report here a straightforward preparation of various nucleoside vinyl disulfides in high yields under mild conditions using the new reaction of vinyl 2-(trimethylsilyl)ethyl (TMSE) sulfides with sulfenyl chlorides. This reaction allows the preparation of various mixed disulfides from stable silyl sulfides without formation of oxidizable and/or unstable thiols. The easy preparation of vinyl disulfides through this reaction should offer new perspectives in vinylthiol chemistry.