Beckman Fellow 2009-10

Oleksii Aksimentiev


Nanopore Electrostatic Tweezers for Single Molecule Manipulation and Detection

In order to understand how protein machinery packages, copies, and transcribes information encoded in the genome, researchers isolate single biomolecules and apply mechanical forces to control or disrupt their function. Several methods have proven successful in this area (e.g., optical tweezers, atomic force microscopy), yet they share the drawback of having a low throughput, which makes it challenging to collect enough data to reconstruct the free-energy profile of a rupture event.

To achieve significantly higher throughput, Professor Aksimentiev’s research group is developing a new method they have termed electrostatic tweezers. The key component is a single, nanometer-diameter pore in a robust, nanometer-thick membrane formed from a metal-oxide-semiconductor capacitor. This method measures the electric current and potential induced by biomolecules while a focused electric field captures and tears apart a protein/DNA complex. The same setup can separate biomolecules according to their electrostatic properties.

The group will simulate the capture of the protein–DNA assemblies by the pore and analyze changes in the ionic current and voltage signals recorded by the electrostatic tweezers. Carrying out a large number of simulations will allow them to calibrate the signals to different stages of the measurement process. They hope to establish measurement protocols that differentiate bounces of protein–DNA complexes and translocations of DNA and proteins not forming a complex from electric field-induced rupture events. The electrostatic tweezers method could be used to detect single nucleotide differences in long stretches of DNA molecules – a significantly improved technology for detecting genetic variations.

During his Center appointment, Professor Aksimentiev will focus on refinements to the simulation approach, integrating the classical molecular dynamics method and the continuum electrostatic solver. His group will then be positioned to take full advantage of the University’s sustained petascale computer Blue Water, which is scheduled to come on line in 2011.