Localized single-stranded bubble mechanism for cyclization of short double helix DNA.

Recent experiments indicate that double-stranded DNA molecules of approximately 100 base pairs in length have a probability of cyclization which is up to 10(5) times larger than that expected based on the known bending modulus of the double-helix. We argue that for short molecules, the formation of a few base pairs of single-stranded DNA can provide a "flexible hinge" that facilitates loop formation. A detailed calculation shows that this mechanism explains the experimental data.