2005/01/17 by Igor M. Kulić, Igor M. Kulic, Hervé Mohrbach +7 · 2 citations
Engineering · Physics and Astronomy · #Force Microscopy Techniques and Applications #Molecular Junctions and Nanostructures #Near-Field Optical Microscopy #cond-mat.soft #cond-mat.stat-mech
paper · pdf · doi:10.1103/physreve.72.041905
4 pages, 2 figures
arxiv created 2005/01/17 · openalex publication_date 2005/10/06 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
We derive the single molecule equation of state (force-extension relation) for DNA molecules bearing sliding loops and deflection defects. Analytical results are obtained in the large force limit by employing an analogy with instantons in quantum mechanical tunneling problems. The results reveal a remarkable feature of sliding loops--an apparent strong reduction of the persistence length. We generalize these results to several other experimentally interesting situations ranging from rigid DNA-protein loops to the problem of anchoring deflections in atomic force microscopy stretching of semiflexible polymers. Expressions relating the force-extension measurements to the underlying loop or boundary deflection geometry are provided and applied to the case of the gal repressor dimer protein. The theoretical predictions are complemented and quantitatively confirmed by molecular dynamics simulations.