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Localized Single-Stranded Bubble Mechanism for Cyclization of Short Double Helix DNA

2004; American Physical Society; Volume: 93; Issue: 10 Linguagem: Inglês

10.1103/physrevlett.93.108108

1092-0145

Jie Yan, John F. Marko,

Genomics and Chromatin Dynamics

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.