Forces on DNA in Confinement as Measured by Optical Tweezers

Abstract

We developed a setup which allows for the stalling of several DNA molecules simultaneously in nanocapillaries with diameters down to 150 nm. Our results demonstrate that the force on DNA molecules are linearly proportional to the number of molecules in the nanocapillary with diameters larger than 500 nm. In contrast, for nanocapillaries with diameters around 150 nm we observe that the force is not scaling linearly with the number of DNA strands but increasess with the square root. Our data is interesting for the modeling of DNA translocation in crowded environments suggesting that inter-molecular spacing is important for the electrophoretic forces. Quantitative modeling and more data for a range of salt concentrations in addition to measurements in smaller and larger nanocapillaries are needed to clarify the force on DNA strands in crowded environments. In the future, our setup is suitable to probe tension and relaxation dynamics of single DNA molecules inside and outside of nanocapillaries. We will also employ our system for the analysis of voltage-driven translocation through protein nanopores or DNA origami nanopores.