(285e) A Simple Model for the Wall Depletion Length of Confined DNA

DNA has been widely used as a model polymer to study the effects of confinement on a semiflexible polymer, which is of particular importance in the field of genome mapping. Theories developed for the stretching of confined DNA agree with simulation predictions but exhibit deviations from experimental observations. One oft-cited rationale for these deviations is the uncertainty in estimating the wall depletion length (δ), a region close to the wall unavailable to the DNA molecule owing to electrostatic repulsions. We examine two theories for the wall depletion length and show that, for ionic strengths of interest for the problem of DNA confinement in a nanochannel, both of these theories simplify to a scaling of the form δ~λ_D, where λ_D is the Debye length. To test this model and determine the prefactor for its scaling, we experimentally measured the wall depletion length for ionic strengths ranging from 15 to 75 mM, using circa 5 million measurements of the fractional extension of E. coli genomic DNA stretched in 38 x 38 nm silica nanochannels and visualized using the BioNano Genomics Irys platform. The depletion length was extracted from the experimental data using the Odijk theory for strong confinement. We indeed found a linear relationship δ~λ_D, thus furnishing a simple yet accurate model for estimating the wall depletion length of confined DNA.