Quantitative Measurements of the Size Scaling of Linear and Circular DNA in Nanofluidic Slitlike Confinement

Abstract

Quantitative size measurements of single linear and circular DNA molecules in nanofluidic slitlike confinement are reported. A novel experimental method using DNA entropophoresis down a nanofluidic staircase implemented comprehensive variation of slitlike confinement around d ≈ 2p, where d is the slit depth and p is the persistence length, throughout the transition from strong to moderate confinement. A new numerical analysis approximated and corrected systematic imaging errors. Together, these advances enabled the first measurement of an experimental scaling relation between the in-plane radius of gyration, R∥, and d, yielding R∥ ∼ d–1/6 for all DNA samples investigated. This differs from the theoretical scaling relation, Re ∼ d–1/4, for the root-mean-square end-to-end size, Re. The use of different labeling ratios also allowed a new test of the influence of fluorescent labels on DNA persistence length. These results improve understanding of the basic physical behavior of polymers confined to nanofluidic slits and inform the design of nanofluidic technology for practical applications.