Force-fluctuation physics of confined DNA: probing the breakdown of the Marko-Siggia law

Abstract

Introduction: The study of polymers in nanofluidic systems such as nanopores and nanochannels is an important avenue of research in the physical and life sciences today. Complex nanofluidic devices containing varying topography are ideal for quantifying the behaviour of polymers under confinement. This study investigates the Marko-Siggia force-extension relationship under confinement. We measure the transverse fluctuations of deoxyribonucleic acid (DNA) confined between two pits in a nanofluidic slit to measure the potential breakdown of this model.

Methods: We took images of fluorescently tagged single DNA molecules in the nanopit array with video- fluorescence microscopy and analyzed the standard deviation of the peak position along the direction of the molecular extension.

Results: We were able to measure the parabolic relation between position and the strength of transverse fluctuations. By examining the peak variance as a function of slit height, our results indicate that the two dimensional version of the force-fluctuation relationship may be appropriate in the limit of strong confinement. However, we could not consistently measure the absolute length of the DNA stretched between two pits, which prevented us from fully exploring the force-extension and force-fluctuation relationships of confined DNA.

Conclusions: These experiments further demonstrate that nanofluidic confinement serves as a useful tool for testing the extreme properties of polymers, and our results suggest further investigation into the breakdown of the Marko-Siggia force law.