Capillary electrophoresis is a sensitive monitor of the hairpin–random coil transition in DNA oligomers

Capillary electrophoresis (CE) has been used to characterize the hairpin–random coil transition of four octamers in the GCxxxxGC minihairpin family, where xxxx is GAAA, TTTC, TTTT, or AAAA. The transition can be monitored by CE because differences in the frictional coefficients of the hairpin and coil forms of each octamer lead to a difference of approximately 9% in the free solution mobilities of the two conformations. The GAAA octamer is unusually stable, with a melting temperature of 65 °C. The TTTT octamer forms a minihairpin with a melting temperature of 29 °C, the TTTC octamer has a melting temperature of 16 °C, and the AAAA octamer has a melting temperature below 0 °C. The thermal transitions of the TTTT, TTTC, and AAAA octamers are well fitted by a structure prediction algorithm; however, the GAAA minihairpin is considerably more stable than predicted. The melting temperature of the GAAA minihairpin is reduced to 47 °C in aqueous buffers containing 7.2 M urea and to 33 °C in buffers containing 7.2 M urea plus 40% (v/v) formamide. The combined results indicate that CE is a sensitive technique for monitoring conformational transitions in small DNA molecules.