title: Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel.
abstract: 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'-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.
authors.affiliation: Rowland Institute, Harvard University, Cambridge, MA 02142, USA.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Mathé
authors.forename: Aleksei
authors.initials: A
authors.lastname: Aksimentiev
authors.forename: David R
authors.initials: DR
authors.lastname: Nelson
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten
authors.forename: Amit
authors.initials: A
authors.lastname: Meller
mesh_terms: D001427:Bacterial Toxins / Q000737:chemistry*; D001483:Base Sequence; D055592:Biophysical Phenomena; D001703:Biophysics; D004277:DNA, Single-Stranded / Q000737:chemistry*; D006460:Hemolysin Proteins / Q000737:chemistry*; D066298:In Vitro Techniques; D007473:Ion Channels / Q000737:chemistry; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D011061:Poly A / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D001427:Bacterial Toxins; D004277:DNA, Single-Stranded; D006460:Hemolysin Proteins; D007473:Ion Channels; C021091:staphylococcal alpha-toxin; D011061:Poly A; C015465:poly(dA)