Measuring the wall depletion length of nanoconfined DNA

Abstract

Efforts to study the polymer physics of DNA confined in nanochannels have been stymied by a lack of consensus regarding its wall depletion length. We have measured this quantity in 38 nm wide, square silicon dioxide nanochannels for five different ionic strengths between 15 mM and 75 mM. Experiments used the Bionano Genomics Irys platform for massively parallel data acquisition, attenuating the effect of the sequence-dependent persistence length and finite-length effects by using nick-labeled genomic DNA with contour length separations of at least 30m (88 325 base pairs) between nick pairs. Over 5 × 10 measurements of the fractional extension were obtained from 39 291 labeled DNA molecules. Analyzing the stretching via Odijk's theory for a strongly confined wormlike chain yielded a linear relationship between the depletion length and the Debye length. This simple linear fit to the experimental data exhibits the same qualitative trend as previously defined analytical models for the depletion length but now quantitatively captures the experimental data.

Diffusion of Short Semiflexible DNA Polymer Chains in Strong and Moderate Confinement

“…An approximate way to account for electrostatic repulsion between the DNA chains and silica/glass surfaces involves the use of an effective depletion length, which decreases the apparent slit height . These effects are less significant in our experiments than in many previous reports because the silica surface charge is significantly reduced by silanization and because the DNA is heavily screened by tetracationic intercalating dye.…”

Nanochannel-Confined TAMRA-Polypyrrole Stained DNA Stretching by Varying the Ionic Strength from Micromolar to Millimolar Concentrations

“…By reducing w/p ratios to 1/4 9 , his simulation predicted X/L approaches the unity more closely. On the other hand, Bhandari et al recently reported X/L = 90.39% in 38 nm square channels when IS = 16.9 ~ 72.2 mM, w/p = 0.13 ~0.22 [49]. Their results follow Equation (11) as shown as shown as X symbols in Figure 5A.…”

“…DNA stretch ratio ( X / L ) dependent on p and w : ( A ) The black line was drawn by Equation (11) and the gray line was down-shifted by 0.13 (Equation (12)). The gray symbols were obtained from other references: X : 38 nm nanochannel experiment [49]; open circles: simulation for p=4w; open diamond: simulation for p=w [50]. The blue line was the best fit for the de Gennes regime (Equation (14)).…”

Free Energy and Dynamics of Annihilation of Topological Defects in Nanoconfined DNA

“…Despite being conceptually different, such approximation proved to be reasonably accurate when comparing simulations to experiment. 30,31 Hence, in interpreting our model results, our simulations are equivalent to running experiments in a channel of size D geo = D + w if excluded-volume effects are to be considered.…”

“…The confinement potential mimics hard wall repulsion that allows the WLC to explore D range in both the X and Y directions regardless of the excluded-volume effects. For an experiment conducted in a channel size D , the physical space accessible to the DNA is reduced by the amount δ to account for electrostatic and excluded-volume interaction with channel walls . Different models were proposed to quantify the wall depletion length δ at varying levels of accuracy. , However, it is common to make the approximation that δ = w , where the excluded volume between a charged rod and a functionalized hard wall is taken to be similar in magnitude to the excluded volume between two charged rods of the same linear charge density when mapped to equivalent neutral rods.…”