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Single Molecule Analysis Using Nanometer-Scale Pores

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John J. Kasianowicz, Ph.D. NIST Physical Measurement Laboratory Gaithersburg, MD USA

Protein nanometer-scale pores are the molecular basis for nerve, muscle and intercellular transport. Over the past two decades, we’ve been exploring their potential for use in detecting, identifying and physically characterizing individual molecules. Our results suggest the method might prove useful for rapid DNA sequencing (1-5), sizing individual molecules in real-time (6-8), studying thermodynamic and kinetic proteins of single molecules (9), and screening for therapeutic agents against lethal toxins (10).

1) Kasianowicz, J.J., et al. 1996. PNAS (USA) 93, 13770-13773

2) Akeson, M., et al. 1999. Biophys. J. 77, 3227-3233

3) Kasianowicz, J.J., et al. 2008. Ann. Rev. Analyt. Chem. 1, 737-766

4) Kumar, S., et al. 2012. Nature Scientific Reports 2, 684​

5) Reiner, J.E., et al. 2012. Chemical Reviews 112, 6431-6451

6) Robertson, J.W.F., et al. 2007. PNAS (USA) 104, 8207-8211

7) Reiner, J.E., et al. 2010. PNAS (USA) 107, 12080-12085

8) Balijepalli, A., et al. 2013. J. Am. Chem. Soc. 135, 7064−7072

9) Reiner, J.E., et al. 2013. J. Am. Chem. Soc. 135, 3087-3094

10) Halverson, K.M., et al. 2005. J. Biol. Chem. 280, 34056–34062

JOHN J . KASIANOWICZ (CV) Dr. John Kasianowicz is the Leader of the Nanobiotechnology Project in the Physical Measurement Laboratory at NIST . He earned a Ph. D. in Physiology & Biophysics from the State University of New York at Stony Brook, a M.A. in Physics from the State University of New York at Stony Brook, and a B.A. in Physics (with Distinction) from Boston University. John was a National Academy of Sciences/National Research Council Research Associate in the Chemical Science and Technology Laboratory at NIST prior to joining the staff and becoming a Leader of the Biomolecular Materials Group. Currently, John directs the research efforts of staff scientists, post-doctoral fellows, and graduate/undergraduate students. Dr. Kasianowicz pioneered research in four principal areas: 1) single molecule characterization, quantification, and identification; 2) nanopore-based DNA sequencing; 3) elucidating the mechanisms of bacterial toxin action, and 4) development of new methods for membrane protein structure determination. His seminal work in these fields opened other areas of investigation (e.g., nanopore-based single molecule force spectroscopy), new conferences dedicated to these subjects, and NIH - and DARPA -based funding initiatives. Several companies (e.g., IBM , Oxford Nanopore, Illumina, Genia Technology, Stratos, Electronic BioSciences, Quantum Biosystems, and Roche) are pursuing John’s applied research to develop practical devices for the electronic detection and characterization of individual biological molecules (including DNA ) with a prospect to construct an ubiquitous and low-cost DNA sequencer. His current major focus is the development of electronic systems to simultaneously quantify many biomarkers (proteins, DNA , RNA, etc.) in single cells, tissue, and blood. This research could have a marked impact on understanding basic cellular mechanisms and aid the development of quantitative personalized medicine. John has published 75 papers (Web of Science: 4751 citations; the top 4 papers have 1365, 538, 306, and 223 citations each, h-index 30; Google Scholar: 6231 citations; the top 4 papers have 1798, 706, 383, and 229 citations each, h-index 35, i10 index 54). His most cited paper is in the top 19 cited publications (out of > 51,000) at NIST /NBS since its inception in 1901, including the work of 4 Nobel Laureates. He has given over 200 invited lectures, seminars, and contributed papers (including 4 keynote addresses and 24 plenary lectures) at conferences and institutions world-wide. John was the lead editor of the book “Structure and Dynamics of Confined Polymers” and he directed a NATO Advanced Research Workshop on Biological, Biophysical and Theoretical Aspects of Polymer Structure and Transport held in Hungary. He organized and co-organized several multidisciplinary international meetings. Dr. Kasianowicz’s contributions have been recognized with several awards and honors. He was named a Fellow of the American Physical Society’s Division of Biological Physics (2010) “for his pioneering contributions to the field of biophysics including the detection, identification, characterization and quantification of biological and chemical polymers, and for the development of a new method for protein structure determination”, The Small Times “Best of Small Tech Researcher of the Year Finalist” (2007), and the Dept. of Commerce Silver Medal (2006) “for pioneering the use of nanopores to electronically probe the structure and function of single biomolecules and for the rapid detection of anthrax toxins”. His work has been highlighted in journals that address a wide range of disciplines including Physics Today 65, 29-31 (2012), Science 336, 534 (2012) and 255, 684 (1992), Nanomedicine 5, 840 (2010), Nature Physics 4, 507 (2008); Analytical Chemistry (p. 4743, July 2007); APS News 16, 8 (February 2007); Science 311, 1544-1546 (2006); The Biological Physicist (The Newsletter of the Division of Biological Physics of the American Physical Society) 1(5), 6-8 (2002); Analytical Chemistry (p. 306A, 1 June 2001), Chemical & Engineering News 79(19), 43 (7 May 2001); and Scientific American (September 1997). In addition, he was recently selected as the Guest Editor of a special issue on “Ion Channels in Disease” in Chemical Reviews. His teaching interests include physics, chemistry, biology, and biophysics. In addition, he enjoys amateur astronomy, hiking, golf, and classical music.

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