title: Retention of nucleic acids in ion-pair reversed-phase high-performance liquid chromatography depends not only on base composition but also on base sequence.
abstract: The study on nucleic acid retention in ion-pair reversed-phase high-performance liquid chromatography mainly focuses on size-dependence, however, other factors influencing retention behaviors have not been comprehensively clarified up to date. In this present work, the retention behaviors of oligonucleotides and double-stranded DNAs were investigated on silica-based C18stationary phase by ion-pair reversed-phase high-performance liquid chromatography. It is found that the retention of oligonucleotides was influenced by base composition and base sequence as well as size, and oligonucleotides prone to self-dimerization have weaker retention than those not prone to self-dimerization but with the same base composition. However, homo-oligonucleotides are suitable for the size-dependent separation as a special case of oligonucleotides. For double-stranded DNAs, the retention is also influenced by base composition and base sequence, as well as size. This may be attributed to the interaction of exposed bases in major or minor grooves with the hydrophobic alky chains of stationary phase. In addition, no specific influence of guanine and cytosine content was confirmed on retention of double-stranded DNAs. Notably, the space effect resulted from the stereostructure of nucleic acids also influences the retention behavior in ion-pair reversed-phase high-performance liquid chromatography.
authors.affiliation: State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, China.
authors.forename: Jun-Qin
authors.initials: JQ
authors.lastname: Qiao
authors.affiliation: State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Liang
authors.affiliation: State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, China.
authors.forename: Lan-Chun
authors.initials: LC
authors.lastname: Wei
authors.affiliation: State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, China.
authors.forename: Zhao-Ming
authors.initials: ZM
authors.lastname: Cao
authors.affiliation: State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, China.
authors.forename: Hong-Zhen
authors.initials: HZ
authors.lastname: Lian
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D002851:Chromatography, High Pressure Liquid; D056148:Chromatography, Reverse-Phase; D009696:Nucleic Acids / Q000737:chemistry*
chemical_list: D009696:Nucleic Acids
keywords: Base composition; Base sequence; Ion-pair chromatography; Nucleic acids; Retention behavior