Measuring the wall depletion length of nanoconfined DNA (2018)

Abstract
Efforts to study the polymer physics of DNA con ned 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 nite-length effects by using nick-labeled E. coli genomic DNA with contour length separations of at least 30 m (88,325 base pairs) between nick pairs. In excess of 5 million measurements of the fractional extension were obtained from 39,291 labeled DNA molecules. Analyzing the stretching via Odijk's theory for a strongly con ned wormlike chain yielded a linear relationship between the depletion length and the Debye length. This simple linear fi t 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.

Funding information
Sponsorship: NIH R01-HG006851