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)
1.5 nm 
-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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