(Invited) All-Electronic Sensing of Single Molecule Dynamics Using Carbon Nanotube Devices

Abstract

Single-molecule techniques eliminate ensemble averaging to reveal the mechanisms, timing, and energetics of individual chemical and biochemical events. Over the past decade, single-molecule science has flourished as new techniques have adopted fluorescent probes, optical traps, and scanning probe microscopy to access the single-molecule limit. Recently, carbon nanotube transistors have been added to this toolkit of single-molecule techniques. As electronic transducers, single-walled carbon nanotubes have the sensitivity to detect single molecular events [1] and the bandwidth to resolve microsecond-duration transients and intermediate states [2]. These characteristics provide exciting new opportunities to monitor and understand complex catalytic cycles such as the biochemical reactions of enzymes. For example, the single molecule kinetics of the Klenow fragment (KF) of polymerase I have recently been studied by bioconjugating KF to nanotube transistors. Continuous recordings of polymerase as it processes various DNA templates have extended through >10,000 bond-forming events, providing new insights into the processivity, kinetic variability, and tolerance of polymerase toward synthetic dNTP analogs [3,4]. In addition to the kinetics, signals generated with some analogs revealed conformational states that do not occur with native dNTPs, helping to explain polymerases’ tolerance for incorporating dNTP analogs. The high resolution of the electronic records illuminate new aspects of polymerase’s catalytic cycle and suggest new opportunities for all-electronic DNA sequencing. [1] Y. Choi, et. al., “Single-Molecule Lysozyme Dynamics Monitored by an Electronic Circuit,” Science 335, 319 (2012). [2] M.V. Akhterov, et. al., "Observing Lysozyme Closing and Opening Motions by High-Resolution Single Molecule Enzymology." ACS Chemical Biology 10, 1495 (2015). [3] T.J. Olsen, et. al., “Electronic Measurements of Single-Molecule Processing by DNA polymerase I (Klenow fragment),” JACS 135, 7855 (2013). [4] K.M. Pugliese, et. al., "Processive Incorporation of Deoxynucleoside Triphosphate Analogs by Single-Molecule DNA Polymerase I (Klenow Fragment) Nanocircuits." JACS 137, 9587 (2015).