Liquid chromatographic separation of oligonucleotides

Abstract Synthetic oligonucleotides have become increasingly important molecules as a part of new developments in the use of aptamers, antisense, and small interfering ribonucleic acid (siRNA) for the treatment of different human diseases. The development of chromatographic separation methods for the quantitative and sensitive analysis of oligonucleotides is a critical part for the advancement of this research area. A typical therapeutic oligonucleotide sample is a short ribonucleic acid (RNA) molecule with about 19–21 nucleotide length (~ 7–8 kDa), or a 21-mer base pair length in double-stranded siRNA (~ 16 kDa). Due to their relatively large sizes and multiple negative charges compared with typical, small molecule pharmaceutical compounds, oligonucleotides can be difficult to analyze with conventional reversed-phase liquid chromatography (RPLC) methods. In this chapter, we provide an overview of liquid chromatographic (LC) separation of oligonucleotides, including anion-exchange, ion-pair reversed-phase, and mixed-mode LC.