Threading Immobilized DNA Molecules Through Solid-State Nanopores

In pursuit of manipulating and controlling DNA translocation speed in voltage biased solid-state nanopores, we designed and constructed an apparatus that can control a DNA molecule moving speed and measure the ionic current change when the DNA is captured and released from the nanopore. The probe tip's position is sensed and controlled by a tuning fork based force sensor and a nanopositioning system. Using this apparatus, we demonstrate DNA translocation rate of >100µs/base or <1nm/ms in silicon nitride nanopores. This rate is 1000 times slower than free DNA translocation through solid-state nanopores reported previously, which could provide enough temporal resolution to read each base on a tethered DNA molecule. We show results of this apparatus for measuring controlled translocations of ds/ss hybrid DNA molecules through solid state nanopores. The ds/ss hybrid DNA is a 48.6 kb double-stranded λ DNA with 1kb single-stranded DNA ligated to one end, and biotinlated oligo ligated to the other end for attaching the hybrid DNA to a probe tip. We further compare the controlled translocation with free translocation of these hybrid DNA molecules through solid state nanopores.