research.

(all my papers and thesis are linked below)


bio.   curriculum vitae.    research.    comics.    writing.    music.    links, etc.

to see my current research, please visit my new lab website.

my most recent experiments involved single molecule biophysical studies with solid-state nanopores.

a nanopore is a small hole (ours are 1-30 nm in diameter) fabricated in a thin membrane of insulating material. this membrane is then used as a barrier between two reservoirs of salt solution, leaving the nanopore the only means by which ionic current can flow from one side to the other. our setup allows us to bring dna tethered to a polystyrene bead (2-3 um diameter) to within a few microns of the nanopore by using a laser trap. because dna is charged in solution, when a bias is applied across the membrane, a single molecule of dna can be pulled into the pore (above). this interrupts the ionic current that can go through and thus the event can be seen in the ionic current measurement (below, upper left). also, since the dna remains tethered, the electrophoretic force on the molecule translates to a motion of the bead itself out of its original position, which can be measured seperately (lower left).

 

      

 

further, once a dna is trapped in the pore, the amount of force being applied can be changed by varying the bias across the membrane. this results in a measureable, real-time movement of the tethering bead. the data above (right) shows this motion, where the bead position ("sum signal") only changes when a dna is in the nanopore. the red lines each represent the trapping of a single dna molecule (so from about 13 s to 17 s, there are two dna molecules in the pore).

i am specifically interested in using this technique to study dna-protein complexes. as a proof of principle, we have begun by investigating the RecA nucleoprtoein complex. RecA is a vital protein in the cell, with a role in double strand dna repair and homologous recombination- we have a version of this protein in our own cells called Rad51. but, for the purposes of our studies, the most important aspect is that RecA is able to cooperatively and stably bind along the entire length of dna, forming a kind of protein sheath around it. upon so doing, the properties of the molecule are changed (diameter, charge) in a measurable way.
 
we first showed that bare dna can be easily distinguished from protein coated dna through translocation and through simple conductance blockades in the optical tweezer setup from above. next, we also measured forces on the nucleoprotein filament, showing essentially that we are able to distinguish molecule 'a' from molecule 'b' in the same system, by both size and charge (fig below). we later even used a variation on the same molecule to produce random protein structure on dna, showing that it is possible to measure local structure along a molecule as it passes through the nanopore. all of these combined point the way toward the future utility of nanopores as epigenetic screening tools.
 
 
there is also much to be learned about the formation of nanopores. we use a transmission electron microscope to 'drill' the holes, and spent some effort studying that process and its effect on nanopore shape and stability.

~

previously, i was working on building and performing measurments on electromechanical devices built on single-walled carbon nanotubes (swnt)- a nanoscale form of carbon that is stronger than steel and has incredible electrical properties. our devices used an individual nanotube as a torsional spring in a paddle device. basically, a nanoscale teeter-totter (below, scale bar 500 nm).

 

we were able to do a number of things with this system, including measuring the torsional stiffness of an individual swnt, measure the effect of applied torsional strain on a swnt electrical transport properties, and build a resonator on a multi-walled nanotube (a slightly bigger kind of nanotube- essentially several swnt wrapped around each other). we were most recently able to make swnt resonator devices and measure their operation by using the strain-transport effect we measured previously.

you can also find out information about all of this past work in my thesis. Be warned, though, it's a big file (~15 megs).

~

a long time ago, i also worked on attaching nanotubes to scanning probe tips in order to improve imaging characteristics. but, like i said, that was a long time ago.