title: Distribution functions, loop formation probabilities, and force-extension relations in a model for short double-stranded DNA molecules.
abstract: We obtain, using transfer-matrix methods, the distribution function P(R) of the end-to-end distance, the loop formation probability, and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the appearance of "bubbles," localized regions of enhanced flexibility associated with the opening of a few base pairs of double-stranded DNA in thermal equilibrium, leads to dramatic changes in P(R) and unusual force-extension curves. An analytic formula for the loop formation probability in the presence of bubbles is proposed. For short heterogeneous chains, we demonstrate a strong dependence of loop formation probabilities on sequence.
authors.affiliation: Department of Physics, Indian Institute of Technology Madras, Chennai 600 036, India. ranjith@physics.iitm.ac.in
authors.forename: P
authors.initials: P
authors.lastname: Ranjith
authors.forename: P B Sunil
authors.initials: PB
authors.lastname: Kumar
authors.forename: Gautam I
authors.initials: GI
authors.lastname: Menon
mesh_terms: D004247:DNA / Q000737:chemistry*; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D004247:DNA