title: Enhanced bubble formation in looped short double-stranded DNA.
abstract: Recent experiments have shown the double-stranded (ds) DNAs readily bend and loop over the scale much shorter than their persistence length (50 nm). In an effort to unveil this seemingly surprising phenomenon, we study the emergence of bubbles in short ds DNA loops by simulating the breathing DNA model. We analyze the bubble size distributions and the melting curves for varying contour lengths, which are critically compared with those of linear DNA of the same lengths. We analytically evaluate the free energies associated with double-strand bending and single-strand bubble formation to explain the simulation data. It is found that in shorter looped DNA the bubbles are more easily initiated and formed to release the large bending energy, giving rise to melting at a lower temperature and a lower contour length.
authors.affiliation: Department of Physics and PCTP, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea. ochul lee@postech.ac.kr
authors.forename: O-chul
authors.initials: OC
authors.lastname: Lee
authors.forename: Wokyung
authors.initials: W
authors.lastname: Sung
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA