Rapid and flexible analytical characterization of oligonucleotides in early drug discovery

Antisense oligonucleotides and small interfering RNA are effective RNA-targeting technologies to modulate gene expression. Early drug discovery programs involve extensive oligonucleotide synthesis and testing in in vitro and in vivo assays, demanding fast and flexible analytical characterization for assessing the oligonucleotide purity prior to testing. Rapid methods and data analysis represent a bottleneck in delivering high-throughput analytical solutions. Here, we present two liquid chromatography-mass spectrometry methods for oligonucleotide molecular weight confirmation, purity assessment and impurity profiling applicable across early drug discovery. A novel high-throughput screening method enables rapid purity checks of hundreds of oligonucleotide samples a day and can be utilized for fraction analysis in anion-exchange purification. A separate in-depth characterization method facilitates purity analysis and detailed impurity profiling of oligonucleotide samples. Both methods incorporate (semi-)automated data processing and reporting tools to deliver fast and high-quality results, supporting the early development of oligonucleotide therapeutics.