@article {70,
	title = {Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel},
	journal = {Proc Natl Acad Sci U S A},
	volume = {102},
	year = {2005},
	month = {2005 Aug 30},
	pages = {12377-82},
	abstract = {<p>We characterize the voltage-driven motion and the free motion of single-stranded DNA (ssDNA) molecules captured inside the approximately 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{\textquoteright}-threaded DNA (in the trans to cis direction) is two times slower than the corresponding 5{\textquoteright}-threaded DNA having the same poly(dA) sequence. Moreover, the ion currents flowing through the blocked pore with either a 3{\textquoteright}-threaded DNA or 5{\textquoteright} 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{\textquoteright} end, assuming an asymmetric conformation. As a result, the bases of a 5{\textquoteright}-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.</p>},
	keywords = {Bacterial Toxins, Base Sequence, Biophysical Phenomena, Biophysics, DNA, Single-Stranded, Hemolysin Proteins, Ion Channels, Models, Molecular, Motion, Nucleic Acid Conformation, Poly A, Thermodynamics},
	issn = {0027-8424},
	doi = {10.1073/pnas.0502947102},
	author = {Math{\'e}, J{\'e}r{\^o}me and Aleksei Aksimentiev and Nelson, David R and Klaus Schulten and Meller, Amit}
}
