Measuring the Confinement Free Energy and Effective Width of Single Polymer Chains via Single-Molecule Tetris

Abstract

We perform single-molecule partitioning measurements of the free energy of chain confinement and selfexclusion as a function of confinement dimension and buffer ionic strength via single-molecule Tetris. Individual DNA chains, confined in a nanoslit with a lattice of embedded nanocavities, partition their contour between the cavities. Changes in device geometry and buffer chemistry lead to changes in the number of cavities occupied. We are able to deduce the confinement free energy difference between the nanocavities and the nanoslit by observing how the number of cavities occupied by a single chain varies as a function of device dimension. These measurements enable us to confirm theoretical predictions for confinement free energy based on worm-like chain formalism and quantify the chain effective width w, providing a direct measure of the size of excluded-volume effect on a single-chain level.

Wall depletion length of a channel-confined polymer

“…Our results suggest that these experiments should be conducted in high ionic strength buffers such that the Debye length is small compared to the confinement length scale. This is indeed the case in previous experiments [14]. It is worthwhile to see how our results translate into relevant experimental systems for DNA.…”

“…As such, we view our results for the depletion length of the mean span and variance as support for previous analyses of experimental data. The situation becomes more complicated when DNA confinement is used to measure the confinement free energy [14]. Our results suggest that these experiments should be conducted in high ionic strength buffers such that the Debye length is small compared to the confinement length scale.…”

“…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].…”

Waves of DNA: Propagating excitations in extended nanoconfined polymers

“…Simple nanochannel structures can be used to extend DNA for analysis for high-throughput genomic mapping [2,3]. There has been increasing interest, however, in the development of devices that feature more complex confinement, devices we term "complex nanofluidic landscapes" [4,5]. These structures, produced by incorporating embedded nanotopography in an open nanoslit, feature regions of locally varying dimensionality and confinement scale, allowing for greater variety of physical phenomena and potential manipulations.…”

“…For example, nanogroove devices feature arrays of parallel grooves embedded in a slit; molecules can be driven in an extended conformation maintained perpendicular to the axis of applied force [6,7]. Nanocavity devices, featuring arrays of nanopits etched in a slit, have been investigated for their utility in molecular self-assembly [4], to control single polymer mobility [8] and diffusion [9], and as a probe of polymer confinement physics [5].…”