Nanotechnology for DNA Sequencing
The information to produce many of the components of the cell such as RNAs and proteins is encoded in the sequence of nucleotides of a cell. Determining the DNA sequence is therefore fundamental to molecular biology and medicine. The most used technique for DNA sequencing has been the dideoxy termination method developed by F. Sanger in a Nobel Prize winning groundbreaking work. Through parallelization, automation and refinement of the established Sanger sequencing method, the Human Genome Project is estimated to have cost $3 billion. Much lower cost methods for DNA sequencing will be required to make genome sequencing feasible for routine healthcare practice.
Many new generation sequencing methods have been developed during the last decade, which represent significant advances over the traditional Sanger sequencing. Amongst them, a method based on threading a DNA molecule through a pore of a diameter of a few nanometers to sequence this molecule while it translocates through the nanopore occupies a privileged place. DNA nanopore sequencing has the advantage of being a real-time single molecule DNA sequencing method with little to no sample preparation and inherently of low-cost.
At least two technical roadblocks prevent implementations of DNA nanopore nucleotide identification by electrical sensor methods. 1) The absence of a reliable approach to control the translocation of DNA through the nanopore. 2) The technical difficulties in making sufficiently small sensors. Our work in this field focuses on solving the challenge of translocation control.
To control the DNA translocation through the nanopore we have proposed a device consisting of a metal/dielectric/metal/dielectric/metal multilayer nano-structure built into the membrane that contains the nanopore. Voltage biases between the electrically addressable metal layers will modulate the electric field inside the nanopore. This device utilizes the interaction of discrete charges along the backbone of a DNA molecule with the modulated electric field to trap DNA in the nanopore with single-base resolution. By cyclically turning on and off these gate voltages, we showed theoretically, and we expect to be able prove experimentally, the plausibility to move DNA through the nanopore at a rate of one nucleotide per cycle. We call this device a DNA transistor, as a DNA current is produced in response to modulation of gate voltages in the device.
The DNA transistor is then a DNA positional controlling platform with single-base-resolution, which could be used in combination with sensor measurements that are under development by us and other research groups. By providing enough dwell time for each DNA nucleotide at the electrodes constituting the sensor, the DNA transistor allows exploration of the best electrical sensor that can resolve the difference between the four DNA nucleotides. In that sense, the DNA transistor paves the way to nanopore-based nucleotide sequencing, and personalized medicine.