AVS 53rd International Symposium
    Nanometer-scale Science and Technology Thursday Sessions
       Session NS+BI-ThM

Invited Paper NS+BI-ThM1
A Nanometer-scale Gene Chip: Detecting Single Molecules of DNA using a Silicon Nanopore

Thursday, November 16, 2006, 8:00 am, Room 2016

Session: Biological and Molecular Applications of Nanoscale Structures
Presenter: G.L. Timp, Beckman Institute
Correspondent: Click to Email

We describe a prospective strategy for reading the encyclopedic information encoded in the genome: using a nanopore in a membrane formed from an MOS-capacitor to sense the charge distribution in a single molecule of DNA. In principle, as DNA permeates the capacitor-membrane through the pore, the electrostatic charge distribution polarizes the capacitor and induces a voltage on the electrodes that can be measured. The sub-nanometer precision available through silicon nanotechnology facilitates the fabrication of this nanometer-scale gene chip, and molecular dynamics provides us with a means to design it and analyze the experimental outcomes. Double-stranded DNA is a highly charged, unusually stiff polymer. And so, the nano-electromechanics of the molecule profoundly affect the design of this detector. Consequently, we have explored the electromechanical properties of DNA using an electric field to force single molecules through synthetic nanopores in ultra-thin silicon membranes. At low electric fields E <200mV/10nm, we observed that single stranded DNA can permeate pores with a radii @>=@0.5nm, while double-stranded DNA only permeates pores with a radius @>=@1.5nm because the diameter of the double helix is about 2nm. For pores <1.5nm-radius, we find a threshold for permeation of double stranded DNA that depends on the electric field and pH. For a 1nm-radius pore, the threshold is E=3.1V/10nm at pH=8.5, which we suppose corresponds to the stretching transition in DNA. The threshold field decreases as pH becomes more acidic, consistent with the destabilization of the double helix, implying that double-stranded DNA melts during an electric field-driven translocation through a 1nm-radius pore. These observations provide us with the opportunity to control the translocation kinetics through the pore and determine the specifications of the pore geometry that optimize the signal-to-noise for detection of single nucleotides.