Internucleotidic bond formation using H-phosphonamidate derivatives and acidic activators

Area of Science:

• Organic Chemistry
• Nucleic Acid Chemistry
• Synthetic Chemistry

Background:

• Oligodeoxynucleotide synthesis is crucial for molecular biology and therapeutics.
• Previous methods relied on heating and lacked additive-free conditions.
• H-phosphonamidate derivatives offer a promising alternative monomer class.

Purpose of the Study:

• To develop a room-temperature synthesis of internucleotidic linkages using H-phosphonamidate monomers.
• To investigate the role of acidic activators and solvent effects in the condensation reaction.
• To explore the utility of heterocyclic amino groups as leaving groups.

Main Methods:

• Reaction of H-phosphonamidate monomers with alcohols in the presence of acidic activators.
• Optimization of reaction conditions including solvent and leaving group.
• Synthesis of dinucleoside phosphorothioate derivatives.
• Molecular orbital calculations to support mechanistic hypotheses.

Main Results:

• Achieved internucleotidic linkage formation at room temperature using acidic activators.
• Demonstrated that pyridine accelerates the condensation reaction.
• Identified heterocyclic amino groups with electronegative atoms (S, O) as effective leaving groups.
• Successfully synthesized dinucleoside phosphorothioate derivatives.

Conclusions:

• The study presents the first example of amino group activation in H-phosphonamidate derivatives using acidic activators.
• Tautomerization to the phosphite form is proposed as a key step, accelerated by pyridine and specific leaving groups.
• Optimized conditions facilitated the synthesis of diverse dinucleoside phosphorothioates.