Scott Knudsen

Education

University of Texas at Austin
Ph.D in Biochemistry: August 2006

Penn State University
B.S in Chemistry: December 1999

Laboratory Experience

Aug. 2006 - present
Manalis Lab, MIT
biosensor development

Sept. 2000 – July 2006
Ellington Lab, UT Austin
In vitro selection, biosensor development

Sept. 1997 – Aug. 2000
Bevilacqua Lab, Penn State University
RNA structure / function

Publications

Burg TP, Godin M, Knudsen SM, Shen W, Carlson G, Foster JS, Babcock K, Manalis SR. 2007. Weighing of biomolecules, single cells and single nanoparticles in fluid. Nature 446: 1066-1069.

Knudsen SM, Lee J, Ellington AD, Savran CA. 2006. Ribozyme-mediated signal augmentation on a mass-sensitive biosensor. J Am Chem Soc 128: 15936-15937.

Garibotti AV, Knudsen SM, Ellington AD, Seeman NC. 2006. Functional DNAzymes organized into two-dimensional arrays. Nano Lett 6:1505-1507.

Knudsen, S.M. & Ellington, A.D. Aptazymes: Allosteric Ribozymes and Deoxyribozymes as Biosensors. Chapter 13, The Aptamer Handbook. (Klussmann, S, ed.) pp. 290-309. (Wiley-VCH, 2006).

Bayer, T.S., Booth, L.N., Knudsen, S.M. & Ellington, A.D. Arginine-rich motifs present multiple interfaces for specific binding by RNA. RNA 11, (2005).

Knudsen, S.M. & Ellington, A.D. Ribozyme deja vu. Nat Struct Mol Biol 11, 301-3 (2004).

Knudsen, S.M., Robertson, M.P. & Ellington, A.D. In vitro selection of ribozymes dependent on peptides for activity. RNA 10, 114-27 (2004).

Savran, C.A., Knudsen, S.M., Ellington, A.D. & Manalis, S.R. Micromechanical detection of proteins using aptamer-based receptor molecules. Anal Chem 76, 3194-8 (2004).

Hesselberth, J.R., Robertson, M.P., Knudsen, S.M. & Ellington, A.D. Simultaneous detection of diverse analytes with an aptazyme ligase array. Anal Biochem 312, 106-12 (2003).

Thompson, K.M., Syrett, H.A., Knudsen, S.M. & Ellington, A.D. Group I aptazymes as genetic regulatory switches. BMC Biotechnol 2, 21 (2002).

Knudsen, S.M., Robertson, M.P. & Ellington, A.D. In vitro selection using modified or unnatural nucleotides. in Current Protocols in Nucleic Acid Chemistry, Vol. 2 (eds. Beaucage, S.L., Bergstrom, D.E., Glick, G.D. & Jones, R.A.) 9.6.1-9.6.21 (John Wiley and Sons, Inc., New York, 2001).

Chadalavada, D.M., Knudsen, S.M., Nakano, S. & Bevilacqua, P.C. A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme. J Mol Biol 301, 349-67 (2000).

Conference Presentations

In vitro selection of peptide-dependent and protein-dependent ribozymes
Astrobiology Science Conference 2002. Mountainview, CA
“Origin of Life / Prebiotic Chemistry” session

Functional nucleic acids as biosensor recognition elements
Biosensors 2004: The 8th World Congress on Biosensors. Granada, Spain
Keynote Presentation, “Natural and Synthetic Receptors for Biosensors” session