Taekjip Ha
Professor of Physics, Center for Biophysics and Computational Biology
Affiliate, Department of Chemistry
Professor Ha received his B.S. degree in physics from Seoul National University, Korea 1990 and his Ph.D. from the University of California at Berkeley in 1996. He was a postdoctoral fellow at the Lawrence Berkeley National Laboratory and at Stanford and was briefly a visiting scientist at the Technical University of Denmark, Lyngby, Denmark. He joined the physics faculty at Illinois in 2000.
Research
We are interested in using physical concepts and experimental techniques to study fundamental questions in molecular biology. The biological systems under study include helicases that unzip DNA, a DNA recombination intermediate called a Holliday junction and its associated enzymes, folding and catalysis of hairpin and VS ribozymes, DNA replication machinery, and chromatin remodeling complexes.
Our main experimental tool is single-molecule fluorescence spectroscopy and microscopy, supported by nano-mechanical tools such as magnetic and optical tweezers. We use modern molecular biology techniques to engineer the molecules with fluorescence tags and tether them to a bio-friendly surface. Then, we shine laser light on each molecule to watch it do its thing. A clever design of such experiments can yield new insights to fundamental biological problems. We also use computational tools extensively, not only to acquire and analyze data, but also to model the problems mathematically, to exploit the genomic databases, and to simulate molecular motions and reactions.
Publications
Rothenberg, E., M.A. Trakselis, S.D. Bell and T. Ha, "MCM fork substrate specificity involves dynamic interaction with the 5' tail", J. Biol. Chem. , published on line ahead of print (2007)
Kim, H.K., I. Rasnik, J. Liu, T. Ha and Y. Lu, "Dissecting metal ion-dependent folding and catalysis of a single DNAzyme", Nature Chemical Biology 28, published on line ahead of print (2007)
Yu, J., T. Ha and K. Schulten, "How Directional Translocation is Regulated in a DNA Helicase Motor", Biophys. J. 23, 11-23 (2007)
Hohng, S., R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley and T. Ha, "Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction", Science 318, 279-283 (2007)
Myong, S., M. M. Bruno, A. M. Pyle and T. Ha, "Spring-loaded Mechanism of DNA Unwinding by HCV NS3 Helicase", Science 317, 513-516 (2007)
Wilson, T. J., M. Nahas, L. Araki, S. Harusawa, T. Ha, D. M. Lilley, "RNA Folding and the Origins of Catalytic Activity in the Hairpin Ribozyme", Blood Cells Mol. Dis. 38(1), 8-14 (2007)
Ha, T., "Need for Speed: Mechanical Regulation of a Replicative Helicase", Cell 129(7), 1249-1250 (2007)
Shirude, P.S., B. Okumus, L. Ying, T. Ha and S. Balasubramanian, "Single Molecule Conformational Analysis of G-Quadruplex Formation in the Promoter DNA Duplex of the Proto-Oncogene C-kit", JACS 129(2), 7484-7485 (2007)
Cisse, I., B. Okumus, C. Joo, T. Ha, "Fueling Protein-DNA Interactions Inside Porous Nanocontainers", PNAS 104, 12646-12650 (2007)
Roy, R. A. G. Kozlov, T. M. Lohman and T. Ha, "Dynamic Structural Rearrangments between DNA Binding Modes of E. coli SSB protein", J. of Mol. Biology 369(5), 1244-1257 (2007)
Arluison, V., S. Hohng, R. Roy, O. Pellegrini, P. Regnier and T. Ha, "Spectroscopic Observation of RNA Chaperone Activities of Hfq in Post-transcriptional Regulation by a Small Non-coding RNA", Nuc. Acids Res. 35, 999-1006 (2007)
Cornish P. and T. Ha, "A Survey of Single Molecule Techniques in Chemical Biology", ACS Chemical Biology 2, 53-61 (2007)
Yoon, T., B. Okumus, F. Zhang, Y.K. Shin and T. Ha, "Multiple Intermediates in SNARE-induced Membrane Fusion", PNAS 103, 19731-19736 (2006)
Rasnik, I., S. A. McKinney, and T. Ha, "Nonblinking and Long-lasting Single Molecule Fluorescence Imaging", Nature Methods 3(11), 891-893 (2006)
Joo, C., S. A McKinney, M. Nakamura, I. Rasnik, S. Myong, and T. Ha, "Real Time Observation of RecA Filament Dynamics with Single Monomer Resolution", Cell 126, 515-527 (2006)
McKinney, S. A., C. Joo, and T. Ha, "Analysis of Single Molecule FRET Trajectories using Hidden Markov Modeling", Biophys. J. 91, 1941-1951 (2006)
Rasnik, I., S. Myong, and T. Ha, "Unraveling Helicase Mechanisms One Molecule at a Time", Nucl. Acids Res. 34, 4225-4231 (2006)
Lin, Y., C. E. Guzman, M. C. McKinney, S. K. Nair, T. Ha, and I. K. O. Cann, "Methanosarcina Acetivorans Flap Endonuclease 1 Activity is Inhibited by a Cognate Single-stranded-DNA-binding Protein", J. Bacteriology 188, 6153-6167 (2006)
Yu, J., T. Ha, and K. Schulten, "Structure-based Model of the Stepping Motor of PcrA Helicase", Biophys. J. 19, 2091-2114 (2006)
Toprak, E., J. Enderlein, Sh. Syed, S. McKinney, R. G. Perschek, T. Ha, Y. E. Goldman, and P. R. Selvin, "Defocused Orientation and Position Imaging (DOPI) of Myosin V", Proc. Nat. Acad. Sci. U.S.A. 103, 6495-6499 (2006)
Myong, S., B. Stevens, and T. Ha, "Bridging Conformational Dynamics and Function using Single-Molecule Spectroscopy", Structure 14, 633-643 (2006)
Buranachai, C., S. A. McKinney, and T. Ha, "Single Molecule Nanometronome", Nano Letters 102, 18938-18943 (2006)
Lee, J. Y., B. Okumus, D. S. Kim, and T. Ha, "Extreme Conformational Diversity in Human Telomeric DNA", Proc. Nat. Acad. Sci. U.S.A. 102, 18938-18943 (2005)
Myong, S., I. Rasnik, C. Joo, T. M. Lohman, and T. Ha, "Repetitive Shuttling of a Motor Protein on DNA", Nature 437, 1321-1325 (2005)
Awards
- Howard Hughes Medical Institute Investigator, 2005
- Alfred P. Sloan Fellowship, 2003
- Beckman Fellow, UIUC Center for Advanced Studies, 2003
- Xerox Faculty Research Award, UIUC, 2003
- Cottrell Scholar Award, 2003
- NSF CAREER Award, 2002
- Fluorescence Young Investigator Award, 2002
- Searle Scholar Award, 2001
- Research Innovation Award, 2001
- Outstanding Young Researcher Award, AKPA, 2001
