Over the past several decades, a variety of imaging techniques have enabled a wide range of studies of the structure, function, and dynamics of molecules at the single-molecule level. However, popular fluorescent single-molecule techniques generally cannot directly resolve temporal changes that occur on sub-millisecond timescales, as imaging times must accommodate the relatively slow rate of photon emission from single fluorophores.
In contrast, non-optical techniques that offer direct transduction to ion or electron flux can enable studies of dynamic single-molecule processes on microsecond or nanosecond timescales. Although electronic single-molecule sensors produce larger signals than fluorescent techniques, they are still weak signals, and it is critical to minimize any measurement noise. Towards this end we are designing compact, low-noise, highly parallel, high-speed sensing platforms which combine new direct electronic single-molecule sensors with state-of-the-art semiconductor systems.
For example, a nanopore sensor is a single nanoscale hole in a thin insulating membrane which separates two aqueous solutions. When a target molecule (such as a strand of DNA) passes through a nanopore, it changes the ionic conductance of the pore, which can be measured as an electrical current. Due to the much higher mobility of small dissolved ions compared to larger analyte molecules, nanopores can produce millions of output ions for each individual molecule measured. We recently designed a high-speed nanopore sensing system which combines thin solid-state nanopores with custom low-noise CMOS preamplifiers in a millimeter-scale platform. The low parasitic capacitance of this system allowed us to measure nanopore signals as brief as 1 microsecond, more than 10 times faster than common arrangements based on commercial patch clamp amplifiers.
In addition, we are developing high-speed single-molecule sensors based on chemically functionalized carbon nanotube field-effect transistors. We electrochemically oxidize a carbon nanotube, creating a single point defect which dominates its electronic transport. A probe molecule can be covalently attached to this defect, and the binding of a target molecule to the probe modulates the electron transport through the nanotube. By electrically monitoring the conductance of the nanotube, we can observe single-molecule binding kinetics at very high bandwidth.
- J. K. Rosenstein, M. Wanunu, C. A. Merchant, M. Drndic, and K. L. Shepard, "Integrated nanopore sensing platform with sub-microsecond temporal resolution," doi:10.1038/nmeth.1932, March 18, 2012.
- S. Sorgenfrei, C.-Y. Chiu, M. Johnston, C. Nuckolls, and K. L. Shepard, "Debye Screening in Single-Molecule Carbon Nanotube Field-Effect Sensors," Nano Letters 11(9), pp. 3739-3743, 2011.
- Jacob Rosenstein, Sebastian Sorgenfrei, and K. L. Shepard, "Noise and Bandwidth Performance of Single-Molecule Biosensors," 2011 Custom Integrated Circuits Conference
- S. Sorgenfrei, C-Y Chiu, R. Gonzalez, Y.-J. Yu, P. Kim, C. Nuckolls, and K. L. Shepard, "Label-free single-molecule detection of DNA hybridization kinetics with a carbon nanotube field-effect transistor," Nature Nanotechnology 6, pp. 126-132, 2011.