Single-molecule dynamics of tethered DNA in shear flow: the effect of viscosity*

Deoxyribonucleic acid (DNA) is a highly charged, semiflexible polymer. Chromosomal DNA is much longer than cell dimensions, and various DNA-binding proteins are involved in compacting and organizing chromosomal DNA in the tiny volume of the cell or nucleus. Single-molecule DNA flow-stretching is a widely employed, powerful technique of investigating the underlying mechanisms of these DNA-binding proteins. Here, we combine experiment and simulation to study the effect of buffer viscosity on DNA flow-stretching and DNA fluctuations. Surface-tethered bacteriophage lambda DNA was stretched by hydrodynamic drag force in a flow cell, and the positions of the free end of the DNA were recorded in real time by tracking a quantum dot labeled at the free end. We found that an increase of buffer viscosity results in an increase of DNA length and a decrease of fluctuations of the freely moving end of the DNA. To better understand our experimental results, we performed extensive Brownian dynamics simulations of a bead-spring chain model of the DNA. Static and dynamic properties of the DNA such as the end-to-end distance and correlation functions were determined as a function of the Weissenberg number, Wi, and the relaxation time, τ, of the polymer. Our simulations agree well with our experimental results for the buffer viscosity.