University of Washington

Nanopore Physics Lab

Research

Our academic research is driven by gaining insight into nanoscale dynamics. Most biological function arises at the angstrom to nanometer length scale and this is where biological sciences and physics have perhaps the biggest overlap. In particular, we have been studying how biological molecules move and interact using DNA translocation through biological pores. This single molecule tool has its charms compared to established techniques such as optical tweezers. It is simple to set up, allows analysis of thousands of molecules in 10 minutes, and also allows us to explore dynamic properties of the molecules in a biologically relevant setting.

On the technical side, this has led us to nanopore sequencing of DNA. In nanopore sequencing, a single stranded DNA molecule is drawn into a pore by an electric field. As the DNA is moves through the pore, its nucleotides modulate the ion current flowing through the pore. Intrinsically, nanopore sequencing is the fastest sequencing method because it directly converts the sequence of a single DNA molecules into an electronic signal.

We are focusing our research on using the protein pore mycobacterium smegmatis porin A (MspA). MspA has an ideal geometry for nanopore DNA sequencing (as well as detection and analysis of other molecules). The entire ion current through the pore focuses in a short and narrow constriction, enabling only the nucleotides (analytes) within the constriction to control the amplitude of the ion current. Before introducing MspA to nanopore DNA sequencing we had to mutate MspA to actually allow DNA to pass through it (Butler et al, 2008). Since DNA passes through all known pores too fast to resolve nucleotide (even with the superior signal with MspA), the speed of the translocation had to be reduced. We were able to show that statically positioned nucleotides could be resolved with high signal-to-noise using MspA (Derrington et al, 2010, Manrao et al, 2011). In 2010 we showed that modified DNA could be sequenced MspA (Derrington et al, 2010) and recently we demonstrated that sequencing of (practically) unmodified DNA is possible by combining a molecular motor with MspA (Manrao et al, 2012).

Address: B033 Physics-Astronomy Building University of Washington 3910 15th Ave. NE Seattle, WA 98195-1560
Update: March 23, 2012