1 Effect of Nanoslit Confinement on the Knotting Probability of 2 Circular DNA

10 ABSTRACT: Monte Carlo simulations are used to study the 11 knotting probability of circular DNA confined in a slit. We 12 systematically vary the slit height, the width, and the contour 13 length of the DNA molecule. We find that the trend in 14 knotting probability with respect to slit height can be 15 monotonic or nonmonotonic, depending on the width and 16 contour length. The nonmonotonic trend is caused by two 17 competing factors: the increase of the effective persistence 18 length and the increase of segment density by slit confinement. 19 These factors are antagonistic, in the sense that the increase in 20 effective persistence length disfavors knot formation, whereas 21 the increase in segment density favors the knotting probability. 22 Our simulation results bring to light the importance of both chain length and width for slit-confined circular DNA and can be 23 used to guide future experiments which aim to produce populations of knotted DNA through cyclization or catalyzed double-24 strand passage reactions in confinement