Quantitative analysis of reptation of partially extended DNA in sub-30 nm nanoslits

TL;DR

This study quantitatively characterizes the reptation behavior of single DNA molecules confined in sub-30 nm nanoslits, revealing tube-like motion under strong confinement and surface interactions, with implications for DNA analysis.

Contribution

It provides the first quantitative analysis of DNA reptation in sub-30 nm nanoslits, highlighting the role of confinement and surface interactions in polymer dynamics.

Findings

Tube-like polymer motion occurs under strong quasi-2D confinement.

Surface modifications significantly influence DNA reptation behavior.

Device surface roughness and dye interactions have minor effects.

Abstract

We observed reptation of single DNA molecules in fused silica nanoslits of sub-30 nm height. The reptation behavior and the effect of confinement are quantitatively characterized using orientation correlation and transverse fluctuation analysis. We show tube-like polymer motion arises for a tense polymer under strong quasi-2D confinement and interaction with surface- passivating polyvinylpyrrolidone (PVP) molecules in nanoslits, while etching- induced device surface roughness, chip bonding materials and DNA-intercalated dye-surface interaction, play minor roles. These findings have strong implications for the effect of surface modification in nanofluidic systems with potential applications for single molecule DNA analysis.