Orientation discrimination of single-stranded DNA inside the α-hemolysin membrane channel

doi:10.1073/pnas.0502947102

Orientation discrimination of single-stranded DNA inside the α-hemolysin membrane channel

^*Rowland Institute, Harvard University, Cambridge, MA 02142; ^†Beckmann Institute, University of Illinois, Urbana, IL 61801; and ^‡Lyman Laboratory of Physics, Harvard University, Cambridge, MA 02138

Edited by Stephen L. Mayo, California Institute of Technology, Pasadena, CA, and approved July 12, 2005 (received for review April 11, 2005)

Abstract

We characterize the voltage-driven motion and the free motion of single-stranded DNA (ssDNA) molecules captured inside the ≈1.5-nm α-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 ≈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.

Footnotes

↵ § To whom correspondence should be addressed. E-mail: meller{at}rowland.harvard.edu.
Author contributions: K.S. and A.M. designed research; J.M., A.A., D.R.N., K.S., and A.M. performed research; J.M., A.A., and A.M. analyzed data; J.M., A.A., D.R.N., K.S., and A.M. wrote the paper; A.A. and K.S. performed molecular dynamics simulations; and D.R.N. performed calculations.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: α-HL, α-hemolysin; MD, molecular dynamics; ssDNA, single-stranded DNA.