Temperature-jump kinetics of the dC-G-T-G-A-A-T-T-C-G-C-G double helix containing a G . T base pair and the dC-G-C-A-G-A-A-T-T-C-G-C-G double helix containing an extra adenine

The kinetics of helix formation were investigated using the temperature-jump technique for the following two molecules: dC-G-T-G-A-A-T-T-C-G-C-G, which forms a double helix containing a G·T base pair(the G·T 12-mer), and dC-G-C-A-G-A-A-T-T-C-G-C-G, which forms a double helix containing an extra adenine (the 13-mer). When data were analyzed in an all-or-none model, the activation energy for the helix association process was 22 ± 4 kcal/mol for the G·T 12-mer and 16 ± 7 kcal/mol for the 13-mer. The activation energy for the helix-dissociation process was 68 ± 2 kcal/mol for the G·T 12-mer and 74 ± 3 kcal/mol for the 13-mer. Rate constants for recombination were near 10⁵s^?1M^?1 in the temperature range from 32 to 47°C; for the dissociation process, the rate constants varied from 1s^?1 near 32°C to 130s^?1 near 47°C. Possible effects of hairpin loops and fraying ends on the above data are discussed.