Nanoconfinement-Induced DNA Reptating Motion and Analogy to Fluctuating Interfaces

Macromolecules in an entangled environment are constrained to wriggle predominantly along a confining tube, giving rise to the so-called reptation or tube-like motion. While the principles of polymer physics were well developed to understand its conformational dynamics, the quantitative characterization of the tube diameter and resulting reptation remains an open question. Here, using highly confined parallel plate geometry nanoslits down to sub-30 nm, we directly observe reptation in a one-dimensional (1D) confined nanoenvironment. We provide a quantitative analysis scheme, by introducing the segmental tangential vector and its associated correlation function, to characterize the strand reptation and connect it to the confinement degree. Our analysis shows that the amplitude of the transverse fluctuations (the virtual 2D “tube”) exhibits the typical scaling of fluctuating interfaces, contact lines, or charge density waves, with a roughness exponent, which depends on the slit height. Our results are shown to lead to less rough DNA profiles in shallower nanoslits. We anticipate our analysis to be a starting point for a more detailed understanding of the relationship between polymer physics and other nonequilibrium physical systems.