DNA confined in nanochannels: Hairpin tightening by entropic depletion

Abstract

A theory is presented of the elongation of double-stranded DNA confined in a nanochannel based on a study of the formation of hairpins. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The DNA in the hairpin remains double-stranded. The free energy of the hairpin is significantly larger than what one would expect if this entropic effect were unimportant. As a result, the distance between hairpins or the global persistence length is often tens of micrometer long and may even reach millimeter sizes for 10 nm thin channels. The hairpin shape and size and the DNA elongation are computed for nanoslits and circular and square nanochannels. A comparison with experiment is given.

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

“…Nevertheless, the absence of global hairpins does not preclude the possibility of small scale bunching of the chain configuration beyond what would be expected from the conformation of a deflection segment. 32 Moreover, while excluded volume does not impact the formation of hairpins for very stiff chains where ξ ≪ 1, 16,22,39 excluded volume does play a role for ξ ≈ 1. 22 At the marginal value of ξ in our experiments, such bunching is possible.…”

“…where g is the global persistence length of the chain, 39 w is the effective width of the backbone (including electrostatic interactions), and D eff = D − w is the cross-sectional width available to the chain. Excluded volume suppresses backfolding when ξ > 1.…”

“…Again, the prefactors in these equations were obtained by simulations, 22,35 and the global persistence length 39 was computed by a formula that accounts for thermal fluctuations. 22 The prediction in Eq.…”

Nanoconfinement-Enhanced Conformational Response of Single DNA Molecules to Changes in Ionic Environment

“…In the regime D, h P, coiling is completely suppressed by the high bending energy [18] and contour can be stored within the polymer only through successive deflections of the polymer from the wall. By using T. Odijk's expression for the contour stored on average between polymer wall deflections [19], it is possible to show that [3,4] …”

Confined nanorods: Jamming due to helical buckling

“…Here the main theoretical thrust is in the direction of understanding the various contributions to the confinement free energy that depend on the size of the confining space and the intrinsic properties of the confined nanorods. The behavior of confined semiflexible polymers is particularly important in this context and has been recently analyzed in detail [8,9]. In many respects this type of problems are mainly centered upon transverse confinement, whereas elastic instabilities described before are due to longitudinal confinement of elastic rods.…”