  Base pair mismatch can relieve mechanical stress in highly strained DNA
molecules, but how it affects their kinetic stability is not known. Using
single-molecule Fluorescence Resonance Energy Transfer (FRET), we measured the
lifetimes of tightly bent DNA loops with and without base pair mismatch.
Surprisingly, for loops captured by stackable sticky ends, the mismatch
decreased the loop lifetime despite reducing the overall bending stress, and
the decrease was largest when the mismatch was placed at the DNA midpoint.
These findings show that base pair mismatch transfers bending stress to the
opposite side of the loop through an allosteric mechanism known as cooperative
kinking. Based on this mechanism, we present a three-state model that explains
the apparent dichotomy between thermodynamic and kinetic stability of DNA
loops.
