Theory for the hydrodynamic and electrophoretic stretch of tethered
B-DNA
Biophysical Journal, 75 (3):
1197--1210 (September 1998)Abstract
We have developed a theory for the extension and force of B-DNA tethered
at a fixed point in a uniform hydrodynamic flow or in a uniform applied
electric field. The chain tethered in an electric field is considered
to be subject to free electrophoresis compensated by free sedimentation
in the opposite direction. This allows the use of results of free
electrophoresis for including the effects of small ions. The force
on the chain is derived for a sequence of ellipsoidal segments, each
twice the persistence length of the wormlike chain. Hydrodynamic
interaction between these segments is based on the long-range limit
of flow around the prolate ellipsoids, as derived from equivalent
Stokes spheres. The chain extension is derived by applying the entropic
elasticity relation of Marko and Siggia (1995 Macromolecules. 28:8759-8770)
to each segment for polymer chains under constant tension. We justify
this procedure by comparing with extension results based on the Boltzmann
averaged orientation of straight, freely jointed segments. Predicted
results agree well with recent extension-flow experiments by Perkins
et al., 1995. Science. 258:83-87, and with electrophoretic stretch
experiments by Smith and Bendich (1990 Biopolymers, 29:1167-1173)
on fluorescently stained B-DNA, We find that the equivalence of hydrodynamic
and electrophoretic stretch, proposed by Long et al. (1996 Phys.
Rev. Lett. 76:3858-3861; 1996 Biopolymers 39:755-759), is valid only
for very small chain deformations, but not in general.