Overview: Oligonucleotides are short strands of nucleotides that are synthesized chemically and have various applications in fields such as diagnostics, therapeutics, and research. An essential analysis is to confirm their sequence and modifications. Mass spectrometry is a powerful analytical technique that can provide structural information about oligonucleotides.
Sample preparation: Prepare a solution of the oligonucleotide in an appropriate solvent, typically a polar solvent like water, or low concentration of organic solvent. The concentration of the solution is better within the range of 1-10 µM.
High-performance liquid chromatography – mass spectrometry (HPLC-MS) analysis: The oligonucleotides are separated using DNAPac high-performance liquid chromatography (HPLC). In the negative mode, the ionized oligonucleotides are analyzed using mass spectrometry to determine the mass-to-charge ratio of the parental and the fragmental ions generated by fragmentation with staged collision energy.
Data analysis: The MS data are analyzed using software tools, such as Biopharma Finder, to determine its sequence as well as the types and localization of modifications.