New Oligodeoxynucleotide Derivatives Containing N-(Sulfonyl)-Phosphoramide Groups

Mesyl Phosphoramidate Oligonucleotides as Potential Splice-Switching Agents: Impact of Backbone Structure on Activity and Intracellular Localization

“…Mesyl (μ) and busyl (β) phosphoramidate oligonucleotides (Table 1) were assembled by automated solid-phase phosphoramidite synthesis replacing aqueous iodine oxidation by Staudinger reaction with either methanesulfonyl azide or 1butanesulfonyl azide (0.5 M in acetonitrile, 40 min at ambient temperature) in each cycle of chain elongation [43,45]. After the completion of the synthesis, the oligonucleotides were cleaved from the polymer support and deprotected by standard ammonia treatment followed by consecutive PAGE and RP-HPLC purification as described previously [46].…”

“…1, 2a) were demonstrated to possess increased specificity, reduced toxicity and improved activity over their PS analogues [42]. The results encouraged us to attempt the design of novel steric blocking oligonucleotides incorporating mesyl phosphoramidate (μ) or their extended chain analogue 1-butanesulfonyl (busyl) phosphoramidate (β) groups [43] as potential splice-switching agents by replacing 2'-deoxynucleosides in the backbone with 2'-O-methylribonucleosides (Fig. 1, 2b) or 2'-O-(2methoxyethyl)ribonucleosides (Fig.…”

Novel Lipid-Oligonucleotide Conjugates Containing Long-Chain Sulfonyl Phosphoramidate Groups: Synthesis and Biological Properties

“…A previously developed methodology of Staudinger reaction-mediated in-line oligonucleotide modification [26][27][28] was employed herein to obtain lipophilic conjugates of oligodeoxynucleotides and siRNAs carrying one or more extended hydrocarbon chains, 4-dodecylphenyl or hexadecyl, attached to the internucleotidic phosphate groups via the (sulfonyl)phosphoramidate linkage, which is hydrolytically stable and carries negative charge under physiological conditions (Figure 1A,B). The scheme allows one to modify any internucleotidic or terminal phosphate group within a DNA or 2 -OMe RNA chain from the 5 -to 3 -end by a facile chemical reaction with a stable sulfonyl azide precursor during automated DNA/RNA assembly without recourse to a special phosphoramidite monomer, which is usually obtained by a multi-step synthesis [18,20,21].…”

“…Oligodeoxynucleotides and siRNAs containing ((4-dodecylphenyl)sulfonyl)phospho ramidate (δ) or (hexadecylsulfonyl)phosphoramidate (η) groups were assembled by automated solid-phase synthesis on a Mermaid MM-12 DNA/RNA synthesizer according to a modified β-cyanoethyl phosphoramidite protocol replacing aqueous iodine oxidation by a Staudinger reaction with either 4-dodecylbenzenesulfonyl azide or 1-hexadecanesulfonyl azide (0.5 M in acetonitrile for (δ) or in acetonitrile-THF (2:1 v/v) for (η), 120 min at ambient temperature) in an appropriate cycle of chain elongation [27,28]. Standard Nprotected 5 -DMTr-3 -β-cyanoethyl-N,N'-phosphoramidites of deoxy, 2 -O-TBDMS-ribo and 2 -O-methylribonucleotides (Sigma-Aldrich Inc., St Louis, MO, USA) and 1000 Å CPG polymer supports (Glen Research Corp, Sterling, VA, USA) were used.…”

“…We describe herein a series of novel DNA and RNA lipid conjugates, which have been chemically modified by one to four long-chain N-(sulfonyl)phosphoramidate groups, namely, [(4-dodecylphenyl)sulfonyl]-phosphoramidate group (δ) or (hexadecylsulfonyl)phosphoramidate group (η) at the internucleotidic position(s) near the 3 -or 5 -end of the oligonucleotide chain (Figure 1). The oligonucleotides were obtained by an automated phosphoramidite solid-phase synthesis protocol that employs the Staudinger reaction between the support-bound phosphite triester and the respective sulfonyl azide instead of usual aqueous iodine oxidation to introduce either of the lipophilic modifications following a previously developed procedure [26][27][28].…”