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.