(565b) Nanopore Sensing - Beyond DNA Sequencing

Nanopores (NPs) are single molecule biosensors, which utilize electrokinetic focusing and transport to detect and characterize unlabeled biomolecules.¹ Controlling and tuning the capture rate and the translocation speed of biomolecules through the NP are crucial features to allow sensing of fine biomolecular features within the experimental bandwidth limitations. In the first part of my lecture I will discuss two physical methods to: (i) enhance the capture rate of DNA molecules into solid-state using salt gradients to enable sensitive sensing down to a few attomoles,² and (ii) slowing down the translocation speed of DNA and proteins through NPs using a novel optoelectronic effect that can be switched on or off in a fraction of a millisecond.³

In the second part of my lecture I will discuss biophysical applications utilizing NPs: (i) barcoding and distinguishing among two highly similar HIV genes using solid-state NPs by incorporation of sequence specific peptide-nucleic acids (PNA) probes⁴; (ii) discrimination among two, unlabeled, Ubiquitin (Ub) protein conformers, which only possess a slightly different 3D structure and having the same amino-acid sequence.⁵ (iii) direct and label-free detection of individual transcription-factors bound to DNA.⁶ The ability to analyze biomolecular complexes, fine features along DNA strands and small proteins in their native folded state at the single molecule level opens up broad opportunities in biomedical research and in biophysics.

References

1. Wanunu, M. & Meller, A. in Laboratory Manual on Single Molecules (eds. Selvin, P. R. & Ha, T.) Cold Spring Harbor Press (2008).

2. Wanunu, M., Morrison, W., Rabin, Y., Grosberg, A. Y. & Meller, A. Electrostatic focusing of unlabeled DNA into nanoscale pores using a salt gradient. Nat Nanotechnol 5, 160â??165 (2010).

3. Di Fiori, N. et al. Optoelectronic control of surface charge and translocation dynamics in solid-state nanopores. Nat Nanotechnol 8, 946â??951 (2013).

4. Singer, A., Rapireddy, S., Ly, D. H. & Meller, A. Electronic barcoding of a viral gene at the single-molecule level. Nano Lett 12, 1722â??1728 (2012).

5. Nir, I., Huttner, D. & Meller, A. Direct Sensing and Discrimination among Ubiquitin and Ubiquitin Chains Using Solid-State Nanopores. Biophys. J. 108, 2340â??2349 (2015).

6. Squires, A., Atas, E. & Meller, A. Nanopore sensing of individual transcription factors bound to DNA. Sci. Rep. 5, 1â??11 (2015).