Vertex Pinning and Stretching of Single Molecule DNA in a Linear Polymer Solution

Abstract

Trapping, linearization, and imaging of single-molecule DNA are of broad interest to both biophysicists who study polymer physics and engineers who build nucleic acid analysis methods such as optical mapping. In this study, single DNA molecules in a neutral linear polymer solution are driven with an axial electric field through microchannels, and their dynamics are studied using fluorescence microscopy. Above a certain threshold electric field, individual DNA molecules become pinned to the channel walls at a vertex on each molecule and are stretched in the direction opposite to electric field. Upon removal of the electric field, pinned DNA molecules undergo relaxation within a few seconds to a Brownian coil around the vertex. After tens of seconds, DNA is released and free to diffuse and electromigrate. The method enables high-quality imaging of single-molecule DNA with high throughput using simple-to-fabricate fluidic structures. The conditions required for trapping dynamics, relaxation dynamics, and the repeatability of vertex pinning are analyzed. It is hypothesized that the neutral linear (non-cross-linked) polymers adsorb to the wall and form scaffolds that trap DNA. Potential hypotheses are discussed based on the empirical findings to explain potential physical mechanism of such unique trapping behavior in a non-crosslinked linear polymer solution.

Keywords: DNA stretching; DNA trapping; microfluidics; single molecule DNA.