Experimental Evidence of Weak Excluded Volume Effects for Nanochannel Confined DNA

Abstract

We present experimental demonstration that weak excluded volume effects arise in DNA nanochannel confinement. In particular, by performing measurements of the variance in chain extension as a function of nanochannel dimension for effective channel size ranging from 305 nm to 453 nm, we show that the scaling of the variance in extension with channel size rejects the de Gennes scaling δ2X ~ D1/3 in favor of δ2X ~ D0 using uncertainty at the 95% confidence level. We also show how simulations and confinement spectroscopy can be combined to reduce molecular weight dispersity effects arising from shearing, photocleavage, and nonuniform staining of DNA.

Wall depletion length of a channel-confined polymer

“…In most cases, experiments compare the mean span and/or the variance obtained in experiments to theory or simulation, for example our recent work using confinement spectroscopy [22,23]. In these cases, the question of the exact value of the depletion length remains an open question for quantitative comparisons [22,23]. However, we cannot ascribe any discrepancy between the experiments and theory (or simulations) to a possible problem with the concept of a depletion length -even if there is double-layer overlap in the experimental system.…”

“…Although there are challenges in using DNA beyond those discussed here, for example the inability to tune the system so that different confinement regimes span multiple decades in channel size [39,74], DNA remains the most convenient model system for studying confined polymers. While it may ultimately prove challenging to use DNA to test the existing models down to the prefactors for the scaling laws [23,25,[41][42][43], there is no better experimental system to directly visualize the effects of confinement at the single molecule level and investigate the universal properties of confined polymers at the scaling level.…”

“…DNA has played a key role in the experimental tests of theories of a polymer confined to a slit [1][2][3][4][5][6][7][8][9][10][11][12][13][14] or a channel [15][16][17][18][19][20][21][22][23][24][25][26][27], in particular the models by de Gennes and coworkers for weak confinement [28,29] and Odijk for strong confinement [30,31]. The key results of this body of work have been summarized in several recent reviews [32][33][34].…”

“…Intercalation also increases the DNA contour length relative to the rise of naked DNA [55]. However, uncertainties in contour length can be minimized by (i) ensuring uniform staining of the DNA [56] and (ii) using funnel-shaped channels that allow one to interrogate the properties the same DNA molecule in a range of confinement [18,22,23,25,57]. For long chains [31], the thermodynamic variables become extensive quantities, so funnel-shaped channels permit a single-molecule test of various scaling laws independent of the contour length.…”

“…From a practical standpoint, it seems reasonable that the depletion length would be of the same order of magnitude as the DNA effective width, as their electrostatic origins are similar, but should be corrected for the different charge densities of DNA and, say, fused silica [32]. In order to begin reconciling the remaining discrepancies between theory and experiments on DNA, for example in recent work on the extended de Gennes regime [23,25], it is worthwhile to revisit the concept of a depletion length for a channel-confined polymer.…”