Single molecule, microfluidic sample preparation for nanopore sensors

A nanopore device is a relatively simple structure consisting of a small pore, usually in a thin membrane, embedded in a microfluidic system.  Typically, a potential difference is applied across the nanopore through an electrolyte to drive molecules, such as DNA, through the pore.  As a molecule physically translocates through the nanopore, the current path through the nanopore is partially blocked and thus the current measured through the voltage source will decrease.  By measuring the transit time and current drop, it is possible to ascertain information about the size, shape and charge of the molecule that translocated through the pore.

There are fundamental limits on how many DNA molecules per unit time can be translocated and thus sensed through a single nanopore device.  A straightforward approach to improve throughput, and thus the number of DNA molecules that can be read or sensed in a given amount of time, is to have multiple nanopores sensing DNA molecules in parallel.  Devices currently on the market, such as those from Oxford Nanopore, currently make use of parallelization to improve throughput.  Additionally, up-concentration or enrichment of DNA (either through electrical or chemical means) in the vicinity of the pore can also increase the rate of translocation events and increase throughput.

A further complication arises when working with long DNA fragments as they can enter a pore folded or in a non-linear conformation, which complicates analysis.  Therefore, methods (using nanostructures in the vicinity of the pore or electrical means) to linearize DNA fragments leading up to the pore can yield improvements in generation of useful data from the sensor.  Some additional sample preparation, such as separation of wanted DNA molecules from unwanted molecules and sorting of DNA fragments by size, leading up to the array of nanopore sensors can also further improve the yield and quality of data from such a sensing device.  Both sorting and separation may be achieved using physical, chemical, or electrical means.

The purpose of this Ph.D. will be to explore microfluidic and nanofluidic structures and devices to aid in sample preparation leading up to a nanopore sensor.  The scope of this topic includes:

• Up-concentration of DNA molecules
• Linearization of the DNA fragments prior to entering the nanopore
• Separation of DNA molecules from unwanted molecules
• Sorting of DNA molecules by size

The student will leverage imec’s nanofabrication facilities and expertise to design and develop devices to fulfill the above functional requirements.  Qualified candidates should come from a physics, engineering, or nanotechnology background.  The work is foreseen to involve design, fabrication, and testing of microfluidic devices.