Virgile Viasnoff

Newly published Paper in Biophysical journal

J.Muzard et al Biophysical Journal, 98,10 2010,2170-2179

Collaboration U.Bockelmann, J.Mathé

DNA Duplexes can enter alphahemolysin pores from both sides.

However when the vestibule is entered first the DNA is hold in front of the stem entrance. Unzipping is then faster.

Abstract: This paper explores the role of some geometrical factors on the electrophoretically driven translocations of macromolecules through nanopores. In the case of asymmetric pores, we show how the entry requirements and the direction of translocation can modify the information content of the blocked ionic current as well as the transduction of the electrophoretic drive into a mechanical force. To address these effects we studied the translocation of single stranded DNA through an asymmetric alphahemolysin pore. Depending on the direction of the translocation, we measure the capacity of the pore to discriminate between both DNA orientations. By unzipping DNA hairpins from both sides of the pores we show that the presence of single strand or double strand in the pore can be discriminated based on ionic current levels. We also show that the  transduction of the electrophoretic drive into a denaturing mechanical force depends on the local geometry of the pore entrance. Eventually we discuss the application of this work to the measurement of energy barriers for DNA unzipping as well as for protein binding and unfolding.