Biopolymers such as DNA can be analyzed with great precision using nanopores, tiny holes approximately 2-30nm in diameter. Naturally occurring nanopores can be found in the form of membrane-spanning protein channels that allow for the flow of ions across a lipid bilayer. New techniques in micro- and nano-fabrication allow us to drill nanopores through solid-state membranes on silicon chips, which are more robust and versatile than their biological counterparts. Because nanopores are of comparable size to DNA, the �threading� of a single molecule through such an opening has measurable electrical effects. These measurements can provide insight into the characteristic properties of DNA, such as folding conformation and molecular size of the strand in question.

We have designed a fluidic device that fills and bathes the nanopore with an ionic solution. When a voltage is applied across the nanopore, a ~nanoampere current of ions flows through the pore. When negatively charged DNA molecules are injected in our system, they are pushed through the nanopore by an electrophoretic force. The DNA blocks a large portion of the pore and impedes the flow of ions through it, producing a measurable current drop that allows us to electrically detect and analyze individual DNA molecules. We show that our nanopore setup is sensitive to folded DNA conformations but is unable to resolve sequence information along an unfolded molecule. However, if DNA is labeled with sequence-specific MIZF binding proteins, a DNA-protein detection scheme could be used to observe primary sequence features along a DNA double helix.