Taekjip Ha University of Illinois at Urbana-Champaign Department of Physics 1110 West Green Street Urbana, IL 61801-3080 Tel: 217-265-0717 • Fax: 217-244-7187 e-mail: tjha at illinois dot edu

- Abbreviated Biographical Data-

• 1996 Ph.D. in physics, University of California at Berkeley, Berkeley, CA [Thesis: Fluorescence Spectroscopy of Single Molecules at Room Temperature and Its Applications (advisors: Shimon Weiss and Daniel Chemla)]
• 1991 M.A. in physics, University of California at Berkeley, Berkeley, CA
• 1990 B.S. in physics, Seoul National University, Seoul, Republic of Korea

EXPERIENCE

• 09/2008-present: Co-director, Center for the Physics of Living Cells, University of Illinois
• 08/2007-present: Professor, Department of Physics, University of Illinois
• 08/2007-present: Professor, Center for Biophysics and Computational Biology, University of Illinois
• 01/2006–present: Affiliate, Beckman Institute, University of Illinois
• 09/2005–present: Investigator, Howard Hughes Medical Institute
• 05/2005–present: Affiliate, Department of Medical Biochemistry, College of Medicine at University of Illinois
• 01/2005–present: Faculty Member of the Precision Proteomics Research Theme, Institute for Genomic Biology, University of Illinois
• 01/2004–present: Affiliate, Department of Chemistry, University of Illinois
• 08/2004–08/2007: Associate Professor, Department of Physics and Center for Biophysics and Computational Biology, University of Illinois
• 08/2000–07/2004: Assistant Professor, Dept of Physics and Center for Biophysics and Computational Biology, University of Illinois
• 01/1998–08/2000: Post-doctoral Fellow (advisor: Steven Chu), Physics Dept, Stanford Univ., Stanford, CA 94305
• 1997 (summer): Visiting Scientist, Technical University of Denmark, Lyngby, Denmark
• 01/1997–12/1997: Post-doctoral Fellow (advisors: Shimon Weiss and Daniel Chemla), Materials Sciences Div., Lawrence Berkeley National Laboratory, Berkeley, CA 94720

RESEARCH INTERESTS

PUBLICATIONS

Publications based on work done prior to moving to the University of Illinois

1. T. Ha, Th. Enderle, D.F. Ogletree, D.S. Chemla, P. Selvin, and S. Weiss, “Probing the interaction between two single molecules: Fluorescence resonance energy transfer between a single donor and a single acceptor ,” Proc. Natl. Acad. Sci. U.S.A. 93, 6264 (1996).
2. T. Ha, Th. Enderle, D.S. Chemla, P. R. Selvin, and S. Weiss, “Single molecule dynamics studied by polarization modulation,” Phys. Rev. Lett. 77, 3979 (1996).
3. T. Ha, D.S. Chemla, Th. Enderle, and S. Weiss, “Single molecule spectroscopy with automated positioning,” Appl. Phys. Lett. 70, 782 (1997).
4. Th. Enderle, T. Ha, D.S. Chemla, C. Magowan, and S. Weiss, “Surface specific mapping and co-localization of malarial and host proteins in red-blood-cell membrane by dual-color near-field scanning optical microscopy,” Proc. Natl. Acad. Sci. U.S.A. 94, 520 (1997).
5. T. Ha, Th. Enderle, D.S. Chemla, and S. Weiss, “Dual-molecule spectroscopy: molecular rulers for the study of biological macromolecules,” IEEE JSTQE 2, 1115 (1996).
6. T. Ha, Th. Enderle, P. R. Selvin, D.S. Chemla, and S. Weiss, “Quantum jumps of single molecules at room temperature,” Chem. Phys. Lett. 271, 1 (1997).
7. T. Ha and D.S. Chemla, Th. Enderle, and S. Weiss, “Strategy for room temperature spectroscopy of single molecules,” Bioimaging 5, 99 (1997).
8. T. Ha, J. Glass, Th. Enderle, D.S. Chemla, and S. Weiss, “Hindered rotational diffusion and rotational jumps of single molecules,” Phys. Rev. Lett. 80, 2093 (1998).
9. Th. Enderle, T. Ha, D.S. Chemla, and S. Weiss, “Near-field fluorescence microscopy of cells,” Ultramicroscopy 71, 303 (1998).
10. U. D. Keil, T. Ha, J. R. Jensen, J. M. Hvam, “Femtosecond tunneling response of surface plasmon polaritons,” Appl. Phys. Lett. 72, 3074 (1998).
11. U. Banin, M. Bruchez, A. P. Alivisatos, T. Ha, S. Weiss, and D.S. Chemla, “Evidence for a thermal contribution to emission intermittency in single CdSe/CdS core/shell nanocrystals,” J. Chem. Phys. 110, 1195 (1999).
12. T. Ha, A. Y. Ting, J. Liang, W. B. Caldwell, A. A. Deniz, D.S. Chemla, P. G. Schultz, and S. Weiss, “Single molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism,” Proc. Natl. Acad. Sci. U.S.A. 96, 893 (1999).
13. A. A. Deniz , M. Dahan, J. Grunwell, T. Ha, A. E. Faulhaber, D. S. Chemla, S. Weiss, and P. G. Schultz, “Single pair FRET on freely diffusing molecules: observation of Förster distance dependence and sub-populations,” Proc. Natl. Acad. Sci. U.S.A. 96, 3670 (1999).
14. T. Ha, A. Y. Ting, J. Liang, A. A. Deniz, D.S. Chemla, P. G. Schultz, and S. Weiss, “Temporal fluctuations of fluorescence resonance energy transfer between two dyes conjugated to a single protein,” Chem. Phys. 247, 107 (1999).
15. M. Dahan, A. A. Deniz, T. Ha, D. S. Chemla, P. G. Schultz, and S. Weiss, “Ratiometric Measurement and Identification of Single Diffusing Molecules,” Chem. Phys. 247, 85 (1999).
16. T. Ha, T. A. Laurence, D. S. Chemla, and S. Weiss, “Polarization Spectroscopy of Single Fluorescent Molecules,” J. Phys. Chem. B 103, 6839 (1999).
17. T. Ha, X. Zhuang, H. D. Kim, J. W. Orr, J. R. Williamson, and S. Chu, “Ligand induced Conformational Changes observed on Single RNA Molecules,” Proc. Natl. Acad. Sci. U.S.A. 96, 9077 (1999).
18. X. Zhuang, L. Bartley, H. P. Babcock, R. Russell, T. Ha, D. Herschlag, and S. Chu, “A Single Molecule Study of RNA Catalysis and Folding,” Science 288, 2048 (2000).
19. X. Zhuang, T. Ha, H. D. Kim, T. Centner, S. Labeit, and S. Chu, “Fluorescence quenching: A tool for single-molecule protein-folding study,” Proc. Natl. Acad. Sci. USA 97, 14241 (2000).
20. H. D. Kim, G. U. Nienhaus, T. Ha, J. W. Orr, J. R. Williamson, and S. Chu, “Mg2+ dependent conformational change of RNA studied by fluorescence correlation on immobilized single molecules,” Proc. Natl. Acad. Sci. USA 99, 4284-4289 (2002).
21. J. Johnson, T. Ha, S. Chu, and S. Boxer, “Initial steps in supported bilayers formation probed by single vesicle assays,” Biophysical J. 83, 3371 (2002).

1. T. Ha, “Single Molecule Fluorescence Resonance Transfer,” Methods 25, 78 (2001).
2. T. Ha, “Single molecule fluorescent methods for nucleic acid studies,” Current Opinion in Structural Biology 11, 287 (2001).
3. T. Ha*, I. Rasnik, W. Cheng, H. P. Babcock, G. Gauss, T. M. Lohman, and S. Chu, “Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase,” Nature 419, 638-641 (2002) *single corresponding author.
4. S.A. McKinney, A. C. Declais, D. M. J. Lilley, and T. Ha, “Structural dynamics of individual Holliday junctions,” Nature Structural Biology 10, 93-97 (2003).
5. T. Ha and J. Xu and, “Photo-destruction intermediates probed by an adjacent reporter molecule,” Phys. Rev. Lett. 90, 223002 (2003)
6. Yildiz, J. Forkey, S.A. McKinney, T. Ha, Y. Goldman and P. R. Selvin, “Myosin V walks hand over hand: Single fluorophore imaging with 1.5 nanometer localization,” Science 300, 2061-2065 (2003)
7. M. C. Murphy, I. Rasnik, W. Cheng, T. M. Lohman and T. Ha, “Probing single stranded DNA conformational flexibility using fluorescence spectroscopy,” Biophysical J. 86, 2530-2537 (2004).
8. E. Tan, T. J. Wilson, M. K. Nahas, R. M. Clegg, D. M. J. Lilley and T. Ha, “A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate,” Proc. Natl. Acad. Sci. USA. 100, 9308 (2003)
9. J.B. Robbins, M. C. Murphy, B.A. White, R.I. Mackie, T. Ha and I. K. O. Cann, “Functional analysis of multiple single-stranded DNA-binding proteins from Methanosarcina acetivorans and their effects of DNA synthesis by PolBI,” J. of Biological Chemistry 279, 6315-26 (2004).
10. S. A. McKinney, E. Tan, T. J. Wilson, M. K. Nahas, A. C. Declais, R. M. Clegg, D. M. J. Lilley and T. Ha, “Single molecule studies of DNA and RNA four-way junctions,” Biochemical Society Transactions 32, 41-45 (2004).
11. S. Hohng, E. Tan, T. J. Wilson, R. M. Clegg, D. M. J. Lilley and T. Ha, “Conformational flexibility of four-way junctions in RNA,” J. of Molecular Biology 336, 69-79 (2004).
12. I. Rasnik, S. Myong, W. Cheng, T. M. Lohman and T. Ha, “DNA-binding orientation and domain conformation of the E. coli Rep helicase monomer bound to a partial duplex junction: Single-molecule studies of fluorescently labeled enzymes,” J. of Molecular Biology 336, 395-408 (2004).
13. B. C. Stevens and T. Ha, “Discrete and heterogeneous rotational dynamics of single membrane probe dyes in gel phase supported bilayers” J. of Chemical Physics 120, 3030-3039 (2004).
14. S. Hohng and T. Ha, “Near-complete suppression of quantum dot blinking in ambient conditions,” J. of American Chemical Society 126, 1324-1325 (2004).
15. C. Joo, S. A. McKinney, D. M. J. Lilley and T. Ha, “Exploring rare conformational species and ionic effects in DNA Holliday junctions using single-molecule spectroscopy,” J. of Molecular Biology 341, 739-751 (2004).
16. T. Ha, “Structural dynamics and processing of nucleic acids revealed by single molecule spectroscopy,” Biochemistry 43, 4055-4063 (2004).
17. M. P. Gordon, T. Ha and P. R. Selvin, “Single Molecule High Resolution Imaging with Photobleaching,” Proc. Natl. Acad. Sci. USA 101, 6462-6465 (2004).
18. S. Hohng, C. Joo and T. Ha, “Single-molecule Three-color FRET,” Biophysical J. 87, 1328-1337 (2004).
19. M. K. Nahas, T. J. Wilson, S. Hohng, K. Jarvie, D. M. J. Lilley and T. Ha, “Observation of internal cleavage and ligation reactions of a ribozyme,” Nature Structural & Molecular Biology 11, 1107-1113 (2004).
20. B. Okumus, T. J. Wilson, D. M. J. Lilley and T. Ha, “Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic,” Biophysical J. 87, 2798-2806 (2004).
21. J. Yu, T. Ha and K. Schulten “Conformational model of the Holliday junction transition deduced from molecular dynamics simulations,” Nucleic Acids Research 32, 6683-6695 (2004).
22. I. Rasnik, S.A. McKinney and T. Ha, “Surfaces and orientations: much to fret about?” Accounts of Chemical Research 38, 542-548 (2005).
23. J. Liu, A. C. Declais, S. A. McKinney, T. Ha, D. G. Norman and D. M. J. Lilley, “Stereospecific effects determine the structure of a four-way DNA junction,” Chemistry & Biology 12, 217-228 (2005).
24. S.A. McKinney, A. Freeman, D. M. J. Lilley and T. Ha, “Observing spontaneous branch migration of Holliday junctions one step at a time,” Proc. Natl. Acad. Sci. USA 102, 5715-5720 (2005).
25. H. Balci, T. Ha, H.L. Sweeney, and P. R. Selvin, “Interhead distance measurements in myosin VI via SHRImP support a simplified hand-over-hand model,” Biophysical J. 89, 413-417 (2005).
26. J. B. Robbins, M. C. McKinney, C. E. Guzman, B. Srinatana, S. Fits-Gibbon, T. Ha and I. K. O. Cann, “The Euryarchaeota: nature's medium for engineering of single-stranded DNA binding proteins,” J. Biol. Chem. 280, 15325-15339 (2005).
27. S. Hohng and T. Ha, “Single-molecule quantum dot FRET,” Chem. Phys. Chem. 6, 956-960 (2005).
28. S. Myong, I. Rasnik, C. Joo, T. M. Lohman and T. Ha, “Repetitive shuttling of a motor protein on DNA,” Nature 437, 1321-1325 (2005).
29. J. Y. Lee, B. Okumus, D.S. Kim and T. Ha, “Extreme conformational diversity of human telomeric DNA,” Proc. Natl. Acad. Sci. USA 102, 18938-18943 (2005).
30. E. Toprak, J. Enderlein, S. Syed, S.A. McKinney, R.G. Petschek, T. Ha, Y. E. Goldman, and P. R. Selvin, “Defocused Orientation and Position Imaging (DOPI) of Myosin V,” Proc. Natl. Acad. Sci. USA 103, 6495-6499 (2006).
31. S. Myong, B.C. Stevens and T. Ha, “Bridging conformational dynamics and function using single-molecule spectroscopy,” Structure 14, 1-11 (2006).
32. C. Buranachai, S.A. McKinney, and T. Ha, “Single molecule nanometronome,” Nano Letters 6, 496-500 (2006).
33. C. Joo, 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, 515-528 (2006).
34. Y. Lin, 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(17), 6153-67 (2006).
35. S.A. McKinney, C. Joo and T. Ha, “Analysis of single molecule FRET trajectories using hidden Markov modeling,” Biophysical J. 91, 1941-1951 (2006).
36. J. Yu, T. Ha and K. Schulten, “Structure-based model of the stepping motor of PcrA helicase,” Biophys. J. 91(6), 2097-2114 (2006).
37. I. Rasnik, S. Myong and T. Ha, “Unraveling helicase mechanism one molecule at a time,” Nucleic Acids Research 34, 4225-4231 (2006).
38. I. Rasnik, S. A. McKinney and T. Ha, “Nonblinking and long-lasting single molecule fluorescence imaging,” Nature Methods 3, 891-893 (2006).
39. T. Y. Yoon, B. Okumus, F. Zhang, Y. K. Shin and T. Ha, “Multiple intermediates in SNARE-induced membrane fusion,” Proc. Natl. Acad. Sci. USA 103, 19731-19736 (2006).
40. V. Arluison, S. Hohng, R. Roy, O. Pellegrini, P. Regnier, T. Ha, “Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA,” Nucleic Acids Research 35 (3), 999-1006 (2007).
41. T. J. Wilson, M. Nahas, L. Araki, S. Harusawa, T. Ha, D. M. Lilly, “RNA folding and the origins of catalytic activity in the hairpin ribozyme,” Blood Cells Mol Dis. 38(1), 8-14 (2007).
42. P. V. Cornish and T. Ha, “A survey of single molecule techniques in chemical biology,” ACS Chemical Biology 2(1), 53-61 (2007).
43. R. Roy, A. Kozlov, T. M. Lohman and T. Ha, “Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein,” J. Mol. Biol. 369, 1244–1257 (2007).
44. P. S. Shirude, 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, 7484-7485 (2007).
45. T. Ha, “Need for speed: Mechanical regulation of a replicative helicase,” Cell 129, 1249-1250 (2007).
46. S. Myong, M. M. Bruno, A. M. Pyle and T. Ha, “Spring-loaded mechanism of DNA unwinding by HCV NS3 helicase,” Science 317, 513-516 (2007).
47. I. Cisse, B. Okumus, C. Joo and T. Ha, “Fueling DNA-protein interactions inside porous nanocontainers,” PNAS 104, 12646-12650 (2007).
48. J. Yu, T. Ha and K. Schulten, “How Directional Translocation is Regulated in a DNA Helicase Motor,” Biophys. J. 93(11), 3783-97(2007).
49. S. Hohng, 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).
50. E. Rothenberg, M. A. Trakselis, S. D. Bell and T. Ha, “MCM fork substrate specificity involves dynamic interaction with the 5’ tail,” J. Biol. Chem. 282, 34229-34234 (2007).
51. H. Kim, I. Rasnik, J. Liu, T. Ha and Y. Lu, “Dissecting metal ion dependent folding and catalysis of single DNAzyme,” Nature Chemical Biology 3, 763-768 (2007).
52. P. R. Selvin and T. Ha, editors, Single Molecule Techniques: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 507 pp., ISBN 978-087969775-4 (2008).
53. C. Joo, H. Balci, Y. Ishisuka, C. Buranachai and T. Ha, “Advances in Single-Molecule Fluorescence Methods for Molecular Biology,” Annual Review of Biochemistry 77, 18.1-18.26 (2008).
54. I. Rasnik, Y. Jeong, S.A. McKinney, V. Rajagopal, S.S. Patel and T. Ha, “Branch migration enzyme as a Brownian Ratchet,” The EMBO J. 27, 1727-1735 (2008).
55. R. Roy, S. Hohng and T. Ha, “A practical guide to single molecule FRET,” Nature Methods 6, 507-516 (2008).
56. G. Q. Tang,  R. Roy, T. Ha, S. S. Patel, “Initial transcription in a single-subunit RNA Polymerase Proceeds through DNA Scrunching and Rotation of the N-terminal Subdomains,” Molecular Cell 30, 567-577 (2008).
57. P. V. Cornish, D. N. Ermolenko, H. F. Noller and T. Ha, “Spontaneous Intersubunit Rotation in Single Ribosomes,” Molecular Cell 30, 578-588 (2008).
58. T. Y. Yoon, X. Lu, J. J. Diao, S. M. Lee, T. Ha and Y. K. Shin, “Single-vesicle analysis reveals strong stimulation of SNARE-mediated membrane fusion by complexin and Ca2+,” Nature Structural & Molecular Biology 15, 707-713 (2008).
59. Z. Su, Y. Ishitsuka, T. Ha and Y.K. Shin, “The SNARE complex from yeast is partially unstructured on the membrane,” Structure 16, 1138-1146 (2008).
60. A. Iqbal, S. Arslan, B. Okumus, T. J. Wilson, G. Giraud, D. G. Norman, T. Ha and D. M. Lilly, “Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids,” Proc Natl Acad Sci, USA, 105(32), 11176-11181 (2008).
61. Y. Lin, L.-J. Lin, P. Sriratana, K. Coleman, T. Ha, M. Spies and I. K. O. Cann, "Engineering of functional replication protein A homologs based on insights in evolution of oligonucleotide/oligosaccharide binding (OB) folds", J. Bacteriology 190(17), 5766-5780 (2008).
62. M. U. Gack, A. Kirchhofer, Y. C. Shin, K. S. Inn, C. Liang, S. Cui, S. Myong, T. Ha, K. P. Hopfner and J. U. Jung, “Roles of RIG-I N-terminal tandem CARD and splice variant in TRIM25-mediated anti-viral signal transduction,” Proc Natl Acad Sci, USA 105(43):16743-16748 (2008).
63. E. Rothenberg, J. M. Grimme, M. Spies and T. Ha, “Human Rad52-mediated homology search and annealing occurs by continuous interactions between overlapping nucleoprotein complexes.” PNAS 205(51), 20274-20279 (2008).
64. S. Myong, S. Cui, P. V. Cornish, A. Kirchhofer, M. U. Gack, J. U. Jung, K. P. Hopfner and T. Ha, Cytosolic viral sensor RIG-I is a 5'-triphosphate-dependent translocase on double-stranded RNA, Science 323(5917):1070-1074 (2009).
65. J. G. Yodh, B.C. Stevens, K. Radhakrishnan, P. Janscak and T. Ha, BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiation. EMBO 28(4):405-416 (2009).
66. P. V. Cornish, D. N. Ermolenko, D.W. Staple, L. Hoang, R.P. Hickerson, H.F. Noller and T. Ha, Following movement of the L1 stalk between three functional states in single ribosome, PNAS 106(8):2571-2576 (2009).
67. D. A. Heller, H. Jin, B. M. Martinez, D. Patel, B. M. Miller, T. K. Yeung, P. V. Jena, C. Höbartner, T. Ha, S. K. Silverman, M. S. Strano, Multimodal optical sensing and analyte specificity using single-walled carbon nanotubes. Nat. Nanotechnol. 4(2):114-120 (2009).
68. Y. Ishitsuka and T. Ha. DNA nanotechnology: a nanomachine goes live, Nat Nanotechnol. 4(5):281-282 (2009).
69. T. Ha, Photonics: How nanocrystals lost their blink, Nature 459 (7247), 649-650 (2009).
70. M. Sorokina M., H-R. Koh, S. S. Patel, T. Ha, Fluoresecent Lifetime Trajectories of a Single Fluorophore Reveal Reaction Intermediates During Transcription Initiation, J Am Chem Soc. 131, 9630–9631 (2009).
71. P. Jena, P Shirude, B. Okumus, K. Laxmi-Reddy, F. Godde, I. Huc, S. Balasubramanian and T. Ha, G-Quadruplex DNA Bound by a Synthetic Ligand is Highly Dynamic, J Am Chem Soc. 131(35):12522-12523 (2009).
72. J. Diao, T. Y. Yoon, Z. Su, Y. K. Shin and T. Ha, C2AB: A Molecular Glue for Lipid Vesicles with a Negatively Charged Surface, Langmuir 25(13), 7177-7180 (2009).
73. B. Okumus, S. Arslan, S. Fengler, S. Myong and T. Ha, Single Molecule Nanocontainers Made Porous Using a Bacterial Toxin, J. Am. Chem. Soc. 131:14844–14849 (2009).
74. M. Honda, J. Park, R. A. Pugh, T. Ha and M. Spies, Single-molecule analysis reveals differential effect of ssDNA-binding proteins on DNA translocation by XPD helicase, Molecular Cell 35:694-703 (2009).
75. R. Roy, A. G. Kozlov, T. M. Lohman and T. Ha, SSB protein diffusion on single-stranded DNA stimulates RecA filament formation, Nature 461(7267), 1092-1097 (2009).