TCB Publications - Abstract

Jerome Mathé, Aleksei Aksimentiev, David R. Nelson, Klaus Schulten, and Amit Meller. Orientation discrimination of single stranded DNA inside the α-hemolysin membrane channel. Proceedings of the National Academy of Sciences, USA, 102:12377-12382, 2005. (PMC: 1194911)

MATH2005 We characterize the voltage-driven and voltage-free motion of single stranded DNA (ssDNA) molecules captured inside the $\sim$ 1.5 nm $\alpha$-Hemolysin pore, and show that the DNA-channel interactions depend strongly on the orientation of the ssDNA molecules with respect to the pore. Remarkably, the voltage free diffusion of the 3 threaded DNA (in the trans to cis direction) is two times slower than the corresponding 5 threaded DNA having the same poly(dA) sequence. Moreover, the ion currents flowing through the blocked pore with either a 3 threaded DNA or 5 DNA differ by approximately 30%. All-atom molecular dynamics simulations of our system reveal a microscopic mechanism for the asymmetric behavior. In a confining pore, the ssDNA straightens and its bases tilt toward the 5 end, assuming an asymmetric conformation. As a result, the bases of a 5-threaded DNA experience larger effective friction, and forced reorientation that favors co-passing of ions. Our results imply that the translocation process through a narrow pore is more complicated than previously believed and involves base tilting and stretching of ssDNA molecules inside the confining pore.

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