From nucleotides to intact transcripts through oligonucleotides: Integrated chromatographic strategies for therapeutic mRNA characterization.

Messenger RNA (mRNA) has emerged as a transformative modality for modern therapeutics, including vaccines and gene therapies. Ensuring the quality, safety, and efficacy of mRNA products requires the evaluation of critical quality attributes (CQAs) such as sequence integrity, nucleotide modifications, purity, and structural stability. The growing complexity of modified mRNA therapeutics highlights the need for robust and orthogonal analytical strategies. This review summarizes liquid chromatography (LC)-based workflows tailored for mRNA characterization including UV detection and mass spectrometry (MS) strategies. These include nucleoside-level analysis to identify chemical modifications and impurities, partial digestion with oligonucleotide mapping to assess sequence coverage and localization of modifications, and intact mRNA analysis to evaluate global structural integrity and encapsulation efficiency. Case studies illustrate practical applications by directly linking analytical workflows to specific CQAs and regulatory-relevant attributes. By leveraging advances in chromatography and mass spectrometry-including bioinert stationary phases, high-resolution detection, and ion-pairing strategies-these studies enable robust analysis of highly polar, charged, and high-molecular-weight mRNA species. The integration of complementary chromatographic and MS-based workflows supports comprehensive characterization, facilitates regulatory compliance, and informs process and formulation development, ultimately providing a coherent framework for quality control in emerging mRNA therapeutics.