Correlated Fluctuations of DNA between Nanofluidic Entropic Traps

• Published in: Macromolecules Vol. 48; no. 13; pp. 4742 - 4747
• Main Authors: Klotz, Alexander R, Mamaev, Mikhail, Duong, Lyndon, de Haan, Hendrick W, Reisner, Walter W
• Format: Journal Article
• Language: English
• Published: American Chemical Society 14.07.2015
• ISSN: 0024-9297; 1520-5835
• DOI: 10.1021/acs.macromol.5b00961

Here we explore thermally driven contour fluctuations within a single DNA chain partitioned between two embedded cavity reservoirs in a nanofluidic slit. Analysis of integrated cavity intensity suggests that contour is exchanged dynamically between the reservoirs via modes that resemble the symmetric and antisymmetric modes of a coupled harmonic oscillator. The relaxation time of the modes is measured as a function of cavity width and spacing. Langevin dynamics simulations reproduce our observations and motivate a free energy model with a blob-type hydrodynamic friction, developed and used to deduce how the measured relaxation times for the modes depend on device parameters. The relaxation time of the antisymmetric mode was found to be consistent with an excluded volume-based stiffness while the faster symmetric mode depends on additional entropic and elastic parameters.