Orientation-dependent interactions of DNA with anα-hemolysin channel

Meni Wanunu, Buddhapriya Chakrabarti, Jérôme Mathé, David R. Nelson, Amit Meller
2008 Physical Review E  
We present experimental and theoretical results on the voltage-dependent escape dynamics of DNA hairpins of different orientations threaded into an ␣-hemolysin channel. Using a coarse-grained formulation, we map the motion of the polymer in the pore to that of a biased single-particle random walk along the translocation coordinate. By fitting the escape probability distributions obtained from theory to experimental data, we extract the voltage-dependent diffusion constants and bias-induced
more » ... ities. Using our two-parameter theory, we obtain excellent agreement with experimentally measured escape time distributions. Further, we find that the ratio of mean escape times for hairpins of different orientations is strongly voltage dependent, with the ratio of 3Ј-to 5Ј-threaded DNA decreasing from Ϸ1.7 to Ϸ1 with increasing assisting voltages V a . We also find that our model describes 5Ј-threaded DNA escape extremely well, while providing inadequate fits for 3Ј escape. Finally, we find that the escape times for both orientations are equal for high assisting voltages, suggesting that the interactions of DNA with the ␣-hemolysin channel are both orientation and voltage dependent.
doi:10.1103/physreve.77.031904 pmid:18517419 fatcat:ar676mkfmvglhcy4kbv3plbqzi