Chromatographic resolution of phosphorothioate (PS) oligonucleotides can be difficult or impossible to resolve by conventional ion-pairing reversed-phase methods. These nucleic acid-based therapeutics represent a new class of biopharmaceutical compounds. Analysis of PS oligonucleotides is becoming more important with the revival of antisense and RNAi-based drugs.
The unique LC/MS method presented in this application note resolves the undesirable failed sequences from the target oligonucleotide peak, and characterizes their respective masses.
Here we use the ACQUITY UPLC System and Oligonucleotide Separation Technology (OST) Columns with MS detection using the Q-Tof Premier Mass Spectrometer.
The exceptional resolution and sensitivity provided by UPLC analysis, used in combination with the high mass accuracy of the Q-Tof Premier, provided an identification of failed phosphorothioate impurities within a 15-minute analysis. Sample throughput has been significantly improved in comparison to HPLC’s 60-minute analysis time.