Aspects of the disclosure relate to liquid chromatography (e.g., HPLC) methods which enable high resolution separations of polynucleotides having hydrophobic portions (e.g., polyadenylated nucleic acids, such as mRNA) based upon the hydrophobic character of the molecules (e.g., polyA tail length). In some embodiments, the disclosure describes liquid chromatographic methods for separating a nucleic acid having a hydrophobic portion (e.g., a polyadenylated nucleic acid, such as an mRNA) from a complex mixture by a mobile phase system that comprises an ion pairing agent selected from Tris, inorganic cations (including e.g., Na, Li, K, ammonium, etc.), biological buffers (e.g., MOPS, HEPES, PIPES, etc.), and other charged or hydrophilic moieties, and lacks conventional ion pairing agents (e.g., Triethylammonium acetate, TEAA). Accordingly, in some embodiments methods described by the disclosure are useful for assessing the quality of pharmaceutical preparations comprising nucleic acids.