Stiffer double-stranded DNA in two-dimensional confinement due to bending anisotropy

Abstract

Using analytical approach and Monte-Carlo (MC) simulations, we study the elastic behaviour of the intrinsically twisted elastic ribbons with bending anisotropy, such as double-stranded DNA (dsDNA), in two-dimensional (2D) confinement. We show that, due to the bending anisotropy, the persistence length of dsDNA in 2D conformations is always greater than 3D conformations. This result is in consistence with the measured values for DNA persistence length in 2D and 3D in equal biological conditions. We also show that in 2D, an anisotropic, intrinsically twisted polymer exhibits an implicit twist-bend coupling, which leads to the kink formations with a half helical turn periodicity along the bent polymer.

Deciphering the mechanical properties of B‐DNA duplex

“…Similarly, cyclization experiments indicate that bending of DNA fragments ~200 bp in size of a “usual” sequence (devoid, e.g., of polypurine tracts or short sequence repeats) is well described by WLC 125 . Theory and MC simulations suggest that, due to the bending anisotropy at short scales (roll is more flexible than tilt), the persistence length of DNA confined to two dimensions (2D) should be about 11% higher than in three dimensions 225 …”

“…125 Theory and MC simulations suggest that, due to the bending anisotropy at short scales (roll is more flexible than tilt), the persistence length of DNA confined to two dimensions (2D) should be about 11% higher than in three dimensions. 225 The standard WLC description is inadequate for molecules with macroscopic curvature, such as phased A-tracts. 164,226 The problem is the static shape, whereas the thermally induced fluctuations may still resemble those of a straight molecule.…”