Controlled sliding of DNA knots in solid-state nanopores

Knots in DNA are useful for investigating the static and dynamic physics of biopolymers in solutions. Recently, we showed nanopores that probe the equilibrium structures of DNA knots in solutions. With unprecedented statistics, our distributions of sizes of equilibrium DNA knots and their positions provide important insights relevant from biological, physical, and technological perspectives. Although nanopores enable statistically significant single molecule investigation, these distributions get biased due to sliding of knots through nanopores, adversely affecting the conclusions. Using our experiments and parametrized simulations, we demonstrate complete control over sliding of knots in nanopores over a molarity range of 1M-3M. We show that controlling the experimental parameters enabled the detection of equilibrium knots in both linear and circular DNA molecules. These results open up an exciting opportunity for statistically significant biophysical investigation of knots in single biomolecules, generating unprecedented insights useful from both scientific and technological perspectives.