Jump to main content
Jump to site search

Volume 139, 2008
Previous Article Next Article

Effect of confinement on properties of stiff biological macromolecules

Author affiliations


The behaviour of semiflexible chains, modelling biopolymers such as DNA and actin in confined spaces, was investigated by means of Monte Carlo simulations. Simulations, based on the coarse-grained worm-like chain (WLC) model, assumed confinement length-scales comparable to those used in micro- and nanofluidic devices. The end-to-end chain elongation R was determined as a function of the channel dimensions and chain bending rigidity. Three regions of chain elongation R, identified in simulations in a cylinder and a slit, were described by current theoretical concepts. In harmony with the measurements of confined DNA, an abrupt transition between the blob region at moderate confinement and the deflection region at strong cylindrical confinement was found. The conditions for hairpin formation were elucidated as a trade-off between confinement and chain stiffness. The intrinsic persistence length of unconfined polymers was calculated by four methods that provided practically identical results. However, in confined geometries only the rigorous and WLC methods predicted the dependence of apparent persistence length P on confinement in a qualitatively correct way. It was found that the simple exponential function, suitable for the description of orientation correlations in free chains is, in confined systems, limited only to short distances along the chain contour and, thus, the apparent persistence length determined by this method just reproduces the intrinsic value of P. The orientation correlations from simulations were compared with analytical predictions in the deflection regime under strong confinement and with the measurements of actin filaments.

Back to tab navigation
Please wait while Download options loads

Publication details

The article was received on 01 Nov 2007, accepted on 04 Dec 2007 and first published on 10 Apr 2008

Article type: Paper
DOI: 10.1039/B716546C
Citation: Faraday Discuss., 2008,139, 377-392
  •   Request permissions

    Effect of confinement on properties of stiff biological macromolecules

    P. Cifra, Z. Benková and T. Bleha, Faraday Discuss., 2008, 139, 377
    DOI: 10.1039/B716546C

Search articles by author