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Sequence-specific oligonucleotide purification using peptide nucleic acid amphiphiles in hydrophobic interaction
James P Vernille1, James W Schneider
1Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213-3890, USA.
Abstract:
We present a methodology to perform sequence-specific separations of oligonucleotides using peptide nucleic acids covalently linked to alkane chains, or "PNA amphiphiles (PNAAs)". The PNAA/DNA duplexes are discriminated from unbound DNA using hydrophobic interaction chromatography on a phenyl-substituted Sepharose column. Nearly quantitative recovery is achieved at concentrations of 50 microM after incubation of oligomers with a stoichiometric amount of PNAA for 1 min or so. The method exhibits high sequence specificity, selectivity, and resolution when applied to mixtures of various oligomers up to 60 base pairs in length.