2004/11/30 by P. Ranjith, P. B. Sunil Kumar, Gautam I. Menon · 3 citations
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #DNA and Nucleic Acid Chemistry #Protein Structure and Dynamics #Spectroscopy and Quantum Chemical Studies #cond-mat.soft #cond-mat.stat-mech #q-bio.BM
paper · pdf · doi:10.1103/physrevlett.94.138102
published as Phys. Rev. Lett. 94, 138102 (2005) · 10 pages
openalex publication_date 2005/04/07 · arxiv created 2005/04/12 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.