Threading Immobilized DNA Molecules through a Solid-State Nanopore at >100 μs per Base Rate

In pursuit of developing solid-state nanopore-based DNA sequencing technology, we have designed and constructed an apparatus that can place a DNA-tethered probe tip near a solid-state nanopore, control the DNA moving speed, and measure the ionic current change when a DNA molecule is captured and released from a nanopore. The probe tip's position is sensed and controlled by a tuning fork based feedback force sensor and a nanopositioning system. Using this newly constructed apparatus, a DNA strand moving rate of >100 mu s/base or <1 nm/ms in silicon nitride nanopores has been accomplished. This rate is 10 times slower than by manipulating DNA-tethered beads using optical tweezers and 1000 times slower than free DNA translocation through solid-state nanopores reported previously, which provides enough temporal resolution to read each base on a tethered DNA molecule using available single-channel recording electronics on the market today. This apparatus can measure three signals simultaneously: ionic current through a nanopore, tip position, and tip vibrational amplitude during the process of a DNA molecule's capture and release by a nanopore. We show results of this apparatus for measuring lambda DNA's capture and release distances and for current blockage signals of lambda DNA molecules biotinylated with one end and with both ends tethered to a tip.