A versatile reagent for the synthesis of 5′-phosphorylated, 5′-thiophosphorylated or 5′-phosphoramidate-conjugated oligonucleotides

Phosphorylating reagent-free synthesis of 5'-phosphate oligonucleotides by controlled oxidative degradation of their 5'-end

The 5'-phosphorylated oligonucleotides (5'-pONs) are currently synthesized using expensive and sensitive modified phosphoramidite reagents. In this work, a simple, cost-effective, efficient, and automatable method is presented, based on the controlled oxidation of the 5'-terminal alcohol followed by a β-elimination reaction. The latter reaction leads to the removal of the terminal 5'-nucleoside and subsequent formation of the 5'-phosphate moiety. Thus, chemical phosphorylation of oligonucleotides (DNA or RNA) is achieved without using modified phosphoramidites.

Oligonucleotide carbohydrate-centered galactosyl cluster conjugates synthesized by click and phosphoramidite chemistries

Oligonucleotide glycoconjugates with a mannose or galactose core bearing four galactose residues introduced by phosphoramidite chemistry and copper catalyzed azide alkyne 1,3-dipolar cycloaddition (click chemistry) have been synthesized. A first click reaction allowed the introduction on a solid support of a mannose core on which four pentynyl linkers were introduced using a phosphoramidite derivative. After the elongation of the oligonucleotide, a second click reaction performed either on solid support or in solution allowed the introduction of four galactose azide derivatives. Repeating the phosphoramidite and click chemistries afforded an oligonucleotide glycoconjugate dendrimer bearing 16 galactoses on its periphery.

5'-Bis-conjugation of oligonucleotides by amidative oxidation and click chemistry

A pent-4-ynyl tert-butyl N,N-diisopropyl phosphoramidite was coupled at the 5'-end of oligonucleotides to give a phosphite triester linkage, which forms an H-phosphonate diester linkage during treatment with dichloroacetic acid. Then an amidative oxidation with CCl(4) in the presence of an amine and a 1,3-dipolar cycloaddition with an azide under copper(I) catalysis afforded the bis-conjugated oligonucleotides with high efficiency. The introduction of a bromoalkyl group as a precursor of azidoalkyl by amidative oxidation allowed the performance of two selective 1,3-dipolar cycloadditions.

Oligonucleotide sequential bis-conjugation via click-oxime and click-Huisgen procedures

A novel procedure has been developed for the bis-conjugation of oligonucleotides using CuAAC (click-H) and oxime (click-O) tethering strategies. Oligonucleotides bearing a 5'-alkyne function and a 3'-aldehyde precursor were synthesized and were bis-conjugated with various reporters including azido carbohydrate or fluorescent dye and aminooxy peptide or carbohydrate. Versatility of the method was demonstrated by performing click-O prior to click-H and vice versa. Interestingly, when click-O is achieved prior to click-H, no purification is required in between, allowing a sequential one-pot protocol.

Azide solid support for 3'-conjugation of oligonucleotides and their circularization by click chemistry

A solid support bearing an azido linker was used to synthesize a 3'-azido-alkyl-oligonucleotide by phosphoramidite chemistry. The resulting oligonucleotide was either conjugated by 1,3-dipolar cycloaddition on solid support or in solution with mannose-propargyl derivative and in solution with dansyl propargyl. Besides, after introduction of an alkyne function at the 5'-end, the resulting oligonucleotide bearing both 3'-azide and 5'-alkyne functions was circularized.

Synthesis of mannose and galactose oligonucleotide conjugates by bi-click chemistry

Glyco oligonucleotide conjugates, each exhibiting two mannose and two galactose residues, were efficiently synthesized by two successive 1,3-dipolar cycloadditions (click chemistry). Two phosphoramidite derivatives were used: one bearing a bromoalkyl group as a precursor to azide functionalization and another bearing a propargyl group. After a first cycloaddition with a mannosyl-azide derivative, the bromine atoms were substituted with NaN(3) and a second click reaction was performed with a 1'-O-propargyl galactose, affording the heteroglyco oligonucleotide conjugate.

Efficient construction of therapeutics, bioconjugates, biomaterials and bioactive surfaces using azide-alkyne "click" chemistry

The concept of "click" chemistry, introduced by Sharpless and coworkers a couple of years ago, promotes the use of efficient, selective and versatile chemical reactions in synthetic chemistry. For instance, the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) is regarded as a prime example of "click" chemistry. This reaction is regioselective, chemoselective and moreover can be performed in aqueous medium at room or physiological temperature. Thus, CuAAC became lately a very popular ligation tool in biological and medical sciences. Several hundred of articles exploring the synthetic possibilities of CuAAC in biosciences have been published within the last four years. The aim of the present review is to give an overall--non exhaustive--picture of this emerging field of research. The advantages and versatility of CuAAC in scientific disciplines as diverse as drug discovery, biochemistry, bioconjugates synthesis, drug-delivery, gene therapy, bioseparation or diagnostics are presented and discussed in detail.

Synthesis of oligonucleotides carrying 5'-5' linkages using copper-catalyzed cycloaddition reactions

There is considerable interest in coupling oligonucleotides to molecules and surfaces. Although amino- and thiol-containing oligonucleotides are being successfully used for this purpose, cycloaddition reactions may offer greater advantages due to their higher chemoselectivity and speed. In this study, copper-catalyzed 1,3-dipolar cycloaddition reactions between oligonucleotides carrying azido and alkyne groups are examined. For this purpose, several protocols for the preparation of oligonucleotides carrying these two groups are described. The non-templated chemical ligation of two oligonucleotides via copper-catalyzed [3+2] cycloaddition is described. By solid-phase methodology, oligonucleotides carrying 5'-5' linkages can be obtained in good yields.

New strategies for cyclization and bicyclization of oligonucleotides by click chemistry assisted by microwaves

The synthesis of cyclic, branched, and bicyclic oligonucleotides was performed by copper-catalyzed azide-alkyne cycloaddition assisted by microwaves in solution and on solid support. For that purpose, new phosphoramidite building blocks and new solid supports were designed to introduce alkyne and bromo functions into the same oligonucleotide by solid-phase synthesis on a DNA synthesizer. The bromine atom was then substituted by sodium azide to yield azide oligonucleotides. Cyclizations were found to be more efficient in solution than on solid support. This method allowed the efficient preparation of cyclic (6- to 20-mers), branched (with one or two dangling sequences), and bicyclic (2 x 10-mers) oligonucleotides.

Conjugation of nucleosides and oligonucleotides by [3+2] cycloaddition

A procedure is presented for copper(I)-catalyzed [3+2] cycloaddition of nucleosides and nucleotides in near-quantitative yield. Azido-alkyne cycloaddition was applied for the preparation of a range of adenosine dimers and derivatives with versatile functionality, as well as for the smooth condensation of two oligonucleotide strands. The described technology may find valuable application in the synthesis of oligonucleotide dimers and conjugates.

Fucosylated Pentaerythrityl Phosphodiester Oligomers (PePOs): Automated Synthesis of DNA-Based Glycoclusters and Binding to Pseudomonas aeruginosa Lectin (PA-IIL)

The synthesis of propargylated pentaerythrityl phosphodiester oligomers (PePOs) was achieved using a DNA synthesizer with a bis-propargylated pentaerythritol-based phosphoramidite. An azido fucose derivative was reacted under "click" chemistry conditions activated by microwaves to construct a series of glycosylated PePOs bearing 4, 6, 8, and 10 L-fucose residues. Binding to the fucose-specific bacterial lectin (PA-IIL) was determined for the fucosylated PePOs through an enzyme-linked lectin amplification competition assay. The IC50 values measured are 10-20 times better than for monovalent l-fucose and denotate for a "macromolecular" effect rather than a "cluster" effect.