Conformational screening of oligonucleotides by variable-temperature high performance liquid chromatography: Dissecting the duplex-hairpin-coil equilibria of d(CGCGAATTCGCG)

Abstract

This study probes the potential of variable-temperature high performance liquid chromatography (VT-HPLC) as a tool for dissecting and modulating nucleic acid structural transitions, using as a model the duplex-hairpin-coil transitions of d(CGCGAATTCGCG). It is demonstrated that VT-HPLC, combined with diode-array detection of the uv signal, enables, for the first time, a physical separation of spectroscopically distinct species that can be assigned to the duplex, hairpin, and coil forms of d(CGCGAATTCGCG). Although the species are spectroscopically distinguishable, they are not readily isolated. Hence, if fractions from the peaks for hairpin or duplex forms are collected and subsequently reinjected onto the cartridge, reequilibration occurs, and both hairpin and duplex peaks are observed. Area integration of the peaks corresponding to duplex and hairpin species provides a means to monitor the duplex to hairpin transition at effective concentrations in the nanomolar range, well below that accessible by conventional spectrophotometers. Concentration-dependent equilibrium constants, melting temperatures, and standard state enthalpies extracted from our measurements compare very well with previous literature results, and with our own results that take into account the effect of our solvent conditions [100 mM TEAA (triethylammonium acetate) and variable acetonitrile] on the melting behavior. By combining precise temperature control with separation based on size, physical behavior, and interaction free energies, VT-HPLC provides a powerful tool for both the modulation and the separation of nucleic acid conformations. © 2004 Wiley Periodicals, Inc.