Tuning the Solubility of Soluble Support Constructs in Liquid Phase Oligonucleotide Synthesis

Area of Science:

• Oligonucleotide Synthesis
• Medicinal Chemistry
• Organic Synthesis

Background:

• Solubility of growing oligonucleotide-soluble support constructs is critical for efficient liquid phase oligonucleotide synthesis (LPOS).
• Poor solubility impacts coupling efficiency, purity, and recovery during oligonucleotide chain elongation.
• Optimizing soluble support constructs is essential for advancing LPOS methodologies.

Purpose of the Study:

• To investigate the impact of different nucleobase protecting groups on the solubility of oligonucleotide-soluble support constructs.
• To evaluate the recovery and yield of protected oligonucleotides synthesized using a tetrapodal soluble support.
• To assess the orthogonality of the 4-oxoheptanedioic acid (OHDA) linker for nucleotide release.

Main Methods:

• Assembly of oligonucleotides on an OHDA linker-derived tetrapodal soluble support.
• Utilized 5'-O-(2-methoxyprop-2-yl)-protected 2'-deoxyribonucleotide phosphoroamidite building blocks with varied nucleobase protecting groups.
• Measured solubility in different solvent systems and antisolvents; evaluated yield and purity using RP HPLC and MS-spectroscopy.

Main Results:

• Tuning nucleobase protecting groups significantly improved construct solubility in aprotic organic solvents.
• Precipitation in 2-propanol yielded near-quantitative recovery of intermediates, with yields ranging from 90% to quantitative.
• Overall yields for synthesized oligonucleotides (up to pentanucleotides) and purity were evaluated, demonstrating successful LPOS.

Conclusions:

• Strategic selection of nucleobase protecting groups is key to enhancing solubility and recovery in LPOS.
• The OHDA linker-derived tetrapodal soluble support facilitates efficient synthesis of oligonucleotides with good yield and purity.
• The orthogonality of the OHDA linker allows for the release of authentic protected nucleotides.