Figure 5.

Three-state DNA cyclization model. A sticky-ended short DNA molecule undergoes a transition between the low FRET (unlooped) state and the high FRET (looped) state. The transition rates between these two FRET states (k₁ and k₂) are governed by the bending energy of DNA. Two different macrostates, teardrop and smooth, can exist within the high FRET state since the looped molecule contains nicks that can spontaneously close and open. Transitions between the teardrop and smooth states occur with rates of k₃ and k₄, and are associated with local transitions of nick closing and opening. For the transition from the teardrop state to the smooth state, integer loops need axial alignment only while half-integer loops need both axial and torsional alignment. Therefore, integer loops can transition to the smooth state more readily than half-integer loops.