Sensing Biomolecules using Nanopores

Nanopores can be used to detect and characterize unlabeled biomolecules, and widely believed to be a main future platform for direct, single molecule sequencing of DNA, RNA and perhaps proteins. Controlling and tuning the translocation speed of biomolecules through nanopores remains to be a main challenge for this technology. We have recently shown¹ that low-power visible light focused at the nano-pore can be used to control its surface charge and thus influence the translocation dynamics of DNA and proteins, by creating a counter electro-osmotic flow in the pore. The optoelectronic effect is analogically tunable on sub-millisecond time scales by simply adjusting the photon density. Specifically, a few mW of green light reduces translocation speed of double-stranded DNA by more than an order of magnitude, by more than two orders of magnitude for small globular proteins such as ubiquitin.

Nanpores can also be used to detect and map DNA and RNA-protein interactions. I will discuss single molecule nanopore measurements of Poly Adenine Binding Proteins (PABPs) associated with translation regulation with poly-Adenine RNAs²,  as well as the interactions of transcription factors with genomic DNA. 

1. 1. Di Fiori, N., Squires, A., Bar, D., Gilboa, T., Moustakas, T. and A. Meller. Optoelectronic control of surface charge andtranslocation dynamics in solid-state nanopores. Nature Nanotechnol 8, 946–951 (2013).
2. 2. Lin, J., Fabian, M., Sonenberg, N. and A. Meller, Nanopore Detachment Kinetics of Poly(A) Binding Proteins from RNA Molecules Reveals the Critical Role of C-Terminus Interactions. Biophysical Journal 102, 1427–1434 (2012).