Taekjip Ha
Professor, University of Illinois
Investigator, Howard Hughes Medical Institute


  

Mailing Address:

1110 West Green Street
Urbana, IL 61801-3080
Tel: 217-265-0717
Fax: 217-244-7187
e-mail: halab_admin@physics.illinois.edu

- Abbreviated Biographical Data-

EDUCATION

EXPERIENCE

RESEARCH INTERESTS

DNA-protein and protein-protein interactions, protein and RNA folding, membrane biophysics, fluorescence microscopy of biological systems, single molecule spectroscopy and manipulations, biologically inspired nano-mechanical devices.

AWARDS

  1. 2011 Ho-Am Prize in Science, Ho-Am Foundation, Korea
  2. 2009 University Scholar, University of Illinois
  3. 2007 Michael and Kate Bárány Award for Young Investigators, Biophysical Society
  4. 2005 Fellow, American Physical Society
  5. 2005 Howard Hughes Medical Institute Investigator
  6. 2004 Participant: Japanese-American National Academy of Engineering Frontiers of Engineering meeting
  7. 2003 Alfred P. Sloan Fellow
  8. 2003 Xerox Faculty Research Award, University of Illinois
  9. 2003 Beckman Fellow at Center for Advanced Studies, University of Illinois
  10. 2003 Cottrell Scholar, Research Corporation
  11. 2002 Fluorescence Young Investigator Award, Biophysical Society
  12. 2002 NSF CAREER Award
  13. 2002 Participant: German-American National Academy of Sciences Frontiers of Science meeting
  14. 2001 Searle Scholars Award
  15. 2001 Research Innovation Award, Research Corporation
  16. 2001 Outstanding Young Researcher Award, AKPA
  17. 1992–1995 Korean Government Scholarship
  18. 1990 University Fellowship, University of California, Berkeley
  19. 1990–1996 Oversea Graduate Fellow, KFAS
  20. 1990 Graduated with High Honors, Seoul National University
  21. 1987–1990 Undergraduate Fellow, KFAS

PUBLICATIONS

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

  1. Ha, T., 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. Ha, T., 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. Ha, T., D.S. Chemla, Th. Enderle, and S. Weiss, Single molecule spectroscopy with automated positioning, Appl. Phys. Lett. 70, 782 (1997).
  4. Enderle, Th., 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. Ha, 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. Ha, T., 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. Ha, T., and D.S. Chemla, Th. Enderle, and S. Weiss, Strategy for room temperature spectroscopy of single molecules, Bioimaging 5, 99 (1997).
  8. Ha, T., 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. Enderle, Th., T. Ha, D.S. Chemla, and S. Weiss, Near-field fluorescence microscopy of cells, Ultramicroscopy 71, 303 (1998).
  10. Keil, U. D., T. Ha, J. R. Jensen, J. M. Hvam, Femtosecond tunneling response of surface plasmon polaritons, Appl. Phys. Lett. 72, 3074 (1998).
  11. Banin, U., 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. Ha, T., 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. Deniz, A. A., 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. Ha, T., 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. Dahan, M., 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. Ha, T., T. A. Laurence, D. S. Chemla, and S. Weiss, Polarization Spectroscopy of Single Fluorescent Molecules, J. Phys. Chem. B 103, 6839 (1999).
  17. Ha, T., 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. Zhuang, X., 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. Zhuang, X., 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. Kim, H. D., 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. Johnson, J., T. Ha, S. Chu, and S. Boxer, Initial steps in supported bilayers formation probed by single vesicle assays, Biophysical J. 83, 3371 (2002).
Independent publications since moving to the University of Illinois
  1. Ha, T., Single Molecule Fluorescence Resonance Transfer, Methods 25, 78 (2001).
  2. Ha, T., Single molecule fluorescent methods for nucleic acid studies, Current Opinion in Structural Biology 11, 287 (2001).
  3. Ha, T.*, 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. McKinney, S.A., A. C. Declais, D. M. J. Lilley, and T. Ha, Structural dynamics of individual Holliday junctions, Nature Structural Biology 10, 93-97 (2003).
  5. Ha, T. 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. Murphy, M. C., 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. Tan, E., 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. Robbins, J.B., 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. McKinney, S. A., 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. Hohng, S., 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. Rasnik, I., 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. Stevens B. C. 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. Hohng S. and T. Ha, Near-complete suppression of quantum dot blinking in ambient conditions, J. of American Chemical Society 126, 1324-1325 (2004).
  15. Joo, C., 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. Ha T., Structural dynamics and processing of nucleic acids revealed by single molecule spectroscopy, Biochemistry 43, 4055-4063 (2004).
  17. Gordon, M. P., T. Ha and P. R. Selvin, Single Molecule High Resolution Imaging with Photobleaching, Proc. Natl. Acad. Sci. USA 101, 6462-6465 (2004).
  18. Hohng, S., C. Joo and T. Ha, Single-molecule Three-color FRET, Biophysical J. 87, 1328-1337 (2004).
  19. Nahas, M. K., 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. Okumus, B., 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. Yu, J., 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. Rasnik, I., S.A. McKinney and T. Ha, Surfaces and orientations: much to fret about? Accounts of Chemical Research 38, 542-548 (2005).
  23. Liu, J., 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. McKinney, S.A., 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. Balci, H., 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. Robbins, J. B., 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. Hohng S. and T. Ha, Single-molecule quantum dot FRET, Chem. Phys. Chem. 6, 956-960 (2005).
  28. 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).
  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. Toprak, E., 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. Myong, S., B.C. Stevens and T. Ha, Bridging conformational dynamics and function using single-molecule spectroscopy, Structure 14, 1-11 (2006).
  32. Buranachai, C., S.A. McKinney, and T. Ha, Single molecule nanometronome, Nano Letters 6, 496-500 (2006).
  33. 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, 515-528 (2006).
  34. 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(17), 6153-67 (2006).
  35. McKinney, S.A., C. Joo and T. Ha, Analysis of single molecule FRET trajectories using hidden Markov modeling, Biophysical J. 91, 1941-1951 (2006).
  36. Yu, J., T. Ha and K. Schulten, Structure-based model of the stepping motor of PcrA helicase, Biophys. J. 91(6), 2097-2114 (2006).
  37. Rasnik, I., S. Myong and T. Ha, Unraveling helicase mechanism one molecule at a time, Nucleic Acids Research 34, 4225-4231 (2006).
  38. Rasnik, I., S. A. McKinney and T. Ha, Nonblinking and long-lasting single molecule fluorescence imaging, Nature Methods 3, 891-893 (2006).
  39. Yoon, T. Y., 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. Arluison, V., 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. Wilson, T. J., 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. Cornish P. V., and T. Ha, A survey of single molecule techniques in chemical biology, ACS Chemical Biology 2(1), 53-61 (2007).
  43. Roy, R., 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. 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, 7484-7485 (2007).
  45. Ha, T., Need for speed: Mechanical regulation of a replicative helicase, Cell 129, 1249-1250 (2007).
  46. 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).
  47. Cisse, I., B. Okumus, C. Joo and T. Ha, Fueling DNA-protein interactions inside porous nanocontainers, PNAS 104, 12646-12650 (2007).
  48. Yu, J., T. Ha and K. Schulten, How Directional Translocation is Regulated in a DNA Helicase Motor, Biophys. J. 93(11), 3783-97(2007).
  49. 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).
  50. 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. 282, 34229-34234 (2007).
  51. Kim, H., 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. Selvin P. R. and T. Ha, editors, Single Molecule Techniques: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 507 pp., ISBN 978-087969775-4 (2008).
  53. Joo, C., 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. Rasnik, I., 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. Roy, R. S., Hohng and T. Ha, A practical guide to single molecule FRET, Nature Methods 6, 507-516 (2008).
  56. Tang,  G. Q., 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. Cornish, P. V., D. N. Ermolenko, H. F. Noller and T. Ha, Spontaneous Intersubunit Rotation in Single Ribosomes, Molecular Cell 30, 578-588 (2008).
  58. Yoon, T. Y., 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. Su, Z,.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. Iqbal, A., 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. Lin, Y., 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. Gack, M. U., 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. Rothenberg, E., J. M. Grimme, M. Spies and T. Ha, Human Rad52-mediated homology search and annealing occurs by continuous interactions between overlapping nucleoprotein complexes. Proc Natl Acad Sci, USA 205(51), 20274-20279 (2008).
  64. Myong, S., 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. Yodh, J. G., 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. Cornish, P. V., 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, Proc Natl Acad Sci, USA 106(8), 2571-2576 (2009).
  67. Heller, D. A., 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. Ishitsuka Y., and T. Ha. DNA nanotechnology: a nanomachine goes live, Nat Nanotechnol. 4(5), 281-282 (2009).
  69. Ha, T., Photonics: How nanocrystals lost their blink, Nature 459 (7247), 649-650 (2009).
  70. Sorokina M., 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. Jena, P., 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. Diao, J., 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. Okumus, B., 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. Honda, M., 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. Roy, R., 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).
  76. Tang, G. Q., R. Roy, R. P. Bandwar, T. Ha and S. S. Patel, Real-time Observation of the Transition from Transcription Initiation to Elongation of the RNA Polymerase, Proc. Natl. Acad. Sci. 106 (52), 22175-22180 (2009).
  77. Pandey, M., S. Syed, I. Donmez, G. Patel, T. Ha and S. S. Patel, Coordinating DNA Replication by Means of Priming Loop and Differential Synthesis Rate, Nature 462 (7275), 940-943 (2009).
  78. Myong, S., and T. Ha, Stepwise Translocation of Nucleic Acid Motors, Current Opinion in Structural Biology 20(1):121-127 (2010) .
  79. Okumus B., and T. Ha, Real-time Observation of G-quadruplex Dynamics using Single Molecule FRET Microscopy, Methods in Molecular Biology 608, 81-96 (2010).
  80. Brenner, M. D., M. S. Scanlan, M. K. Nahas, T. Ha and S. K. Silverman, Multi-Vector Fluorescence Analysis of the xpt Guanine Riboswitch Aptamer Domain and the Conformational Role of Guanine, Biochemistry 49(8), 1596-1605. Erratum in: Biochemistry 16, 49(10), 2306 (2010).
  81. Rothenberg, E. and T. Ha, Single-Molecule FRET Analysis of Helicase Functions, Methods Mol Biol. 587, 29-43 (2010).
  82. Shi, X., J. Lim, and T. Ha, Acidification of the oxygen scavenging system in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe. Anal Chem. 82(14):6132-6138 (2010).
  83. Grimme, J. M, .M. Honda, R. Y. Wright, Y. Okuno, E. Rothenberg, A. V. Mazin, T. Ha and M. Spies, Human Rad52 Binds and Wraps Single-stranded DNA and Mediates Annealing Via Two hRad52-ssDNA Complexes, Nucleic Acids Research 38(9), 2917-2930 (2010).
  84. Diao, J., Z. Su, X. Lu, T. Y. Yoon, Y. K. Shin and T. Ha, Single-Vesicle Fusion Assay Reveals Munc18-1 Binding to the SNARE Core is Sufficient for Stimulating Membrane Fusion, ACS Chemical Neuroscience 17 1(3), 168-174 (2010).
  85. Liu, Y., J. Park, K. A. Dahmen, Y. R. Chemla, and T. Ha, A Comparative Study of Multivariate and Univariate Hidden Markov Modelings in Time-Binned Single-Molecule FRET Data Analysis, J. Phys Chem. B. 114(16), 5386-5403 (2010).
  86. Spies M. and T. Ha, Inching Over Hurdles: How Helicases Move on Crowded Lattices, Cell Cycle 9(9), 1742-1749 (2010).
  87. Grashoff, C., B. D. Hoffman, M. D. Brenner, R. Zhou, M. Parsons, M. T. Yang, M. A. McLean, S. G. Sligar, C. S. Chen, T. Ha and M. A. Schwartz, Measuring Mechanical Tension Across Vinculin Reveals Regulation of Focal Adhesion Dynamics, Nature 466, 263-266 (2010).
  88. Kim, S. K., T. Ha, J. P. Schermann, Biomolecular Structures: From Isolated Molecules to the Cell Crowded Medium. Phys Chem Chem Phys. 12(14):3334-5 (2010).
  89. Kim, S. K., T. Ha, J. P. Schermann. Water in biological systems, Phys Chem Chem Phys. 12(35):10145-6 (2010).
  90. Zhou, R., M. Schlierf and T. Ha, Force-Fluorescence Spectroscopy at the Single-Molecule Level, Methods in Enzymology 475C, 405-426 (2010).
  91. Park, J., S. Myong, A. Niedziela-Majka, K-S. Liu, J. Yu, T. M. Lohman and T. Ha, PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps, Cell 142, 544-555 (2010).
  92. Park, J. and T. Ha, Single Molecule FRET using TIR Microscopy, in Optical Imaging Techniques: A Laboratory Manual, Cold Spring Harbor (2010).
  93. Trabuco, L. G., E. Schreiner, J. Eargle, P. Cornish, T. Ha, Z. Luthey-Schulten, K. Schulten, The role of L1 stalk : tRNA interaction in the ribosome elongation cycle, J. of Molecular Biology 402(4), 741-760 (2010).
  94. Yodh, J. G., M. Schlierf and T. Ha, Insight into helicase mechanism and function revealed through single-molecule approaches, Quarterly Reviews of Biophysics 43(02), 185-217 (2010).
  95. Ishitsuka, Y., B. Okumus, S. Arslan, K. H. Chen and T. Ha, Temperature-Independent Porous Nanocontainers for Single-Molecule Fluorescence Studies, Analytical Chemistry, 82(23), 9694–9701 (2010).
  96. Diao, J., Z. Su, Y. Ishitsuka, B. Lu, K S. Lee, Y. Lai, Y. J. Shin and T. Ha. A single-vesicle content mixing assay for SNARE-mediated membrane fusion, Nat. Commun. 1(5), 1-6 (2010).
  97. Tomko, E. J., H. Jia, J. Park, N. K. Maluf, T. Ha and T. M. Lohman, 5' Single-stranded/duplex DNA junctions are loading sites for E. coli UvrD translocase, EMBO J, 29, 3826-3839 (2010) .
  98. Lee, G., S. Hartung, K.P. Hopfner and T. Ha, Reversible and controllable nano-locomotion of an RNA-processing machinery, Nano Letters 10(12), 5123-5130 (2010) .
  99. Lee, J., S. Lee, K. Ragunathan, C. Joo, T. Ha and S. Hohng, Single-molecule four-color FRET, Angew. Chem. Int. Ed. 49(51), 9922-9925 (2010).
  100. Kim, S. K., T. Ha, and J. P. Schermann, Homochirality and the origin of life. Editorial of the PCCP themed issue, Phys. Chem. Chem. Phys. 13(3), 804-805 (2011).
  101. Brenner, M. D., R. Zhou and T. Ha, Forcing a connection: Impacts of single-molecule force spectroscopy on in vivo tension sensing, Biopolymers 95 (5), 332-344 (2011).
  102. Shi, X. and T. Ha, Seeing a molecular machine self-renew, Proc. Natl. Acad. Sci. USA 1, 108(9), 3584-3589 (2011).
  103. Comstock, M. J., T. Ha and Y. R. Chemla, Ultra-high resolution optical trap with single fluorophore sensitivity, Nature Methods 8, 335–340 (2011).
  104. Liu., C., M. C. McKinney, Y.H. Chen, T. M. Earnest, X. Shi, Li. J. Lin, Y. Ishino, K. Dahmen, I. K.O. Cann and T. Ha, Reverse-Chaperoning Activity of an AAA+ Protein, Biophysical J. 100, 1344-1352 (2011).
  105. Lee, G., J. Yoo, B. J. Leslie, T. Ha, Single-molecule analysis reveals three phases of DNA degradation by an exonuclease. Nat Chem Biol. 7(6), 367-74 (2011).
  106. Kim, S. K., T. Ha T, J. P. Schermann, Editorial on nanobiology. Phys Chem Chem Phys. 7, 13(21), 9916-9917 (2011).
  107. Zhang, Z., V. I. Kottadiel, R. Vafabakhsh, L. Dai, Y. R. Chemla, T. Ha, V. B. Rao, A promiscuous DNA packaging machine from bacteriophage T4. PLoS Biol. 15;9(2), e1000592 (2011).
  108. A. Jain, R. Liu, B. Ramani, E. Arauz, Y. Ishitsuka, K. Ragunathan, J. Park, J. Chen, Y. K. Xiang and T. Ha, Probing cellular protein complexes using single-molecule pull-down, Nature 473, 484-488 (2011).
  109. Lamboy, J. A., H. Kim, K. S. Lee, T. Ha and E. A. Komives, Visualization of the nanospring dynamics of the IκBα ankyrin repeat domain in real time, Proc Natl Acad Sci USA, 108(25), 10178-83 (2011).
  110. Yang, S. Y., X. Shi, S. Park, S. Doganay, T. Ha and S. C. Zimmerman, Monovalent, Clickable, Uncharged, Water-Soluble Perylenediimide-Cored Dendrimers for Target-Specific Fluorescent Biolabeling, J. Amer. Chem. Soc., 133 (26), 9964-9967 (2011).
  111. Jia, H., S. Korolev, A. Niedziela-Majka, N. K. Maluf, G. H. Gauss, S. Myong, T. Ha, G. Waksman and T. M. Lohman, Rotations of the 2B Sub-domain of E. coli UvrD Helicase/Translocase Coupled to Nucleotide and DNA Binding, J. Mol. Biol., 411(3), 633–648 (2011).
  112. Zhou, R., A. G. Kozlov, R. Roy, J. Zhang, S. Korolev, T. M. Lohman and T. Ha, SSB Functions as a Sliding Platform that Migrates on DNA via Reptation, Cell 146, 222-232 (2011).
  113. Honda, M., Y. Okuno, J. Yoo, T. Ha and M. Spies, Tyrosine phosphorylation enhances RAD52-mediated annealing by modulating its DNA binding, EMBO Journal 30, 3368-3382 (2011).
  114. Ragunathan, K., C. Joo and T. Ha, Real-Time Observation of Strand Exchange Reaction with High Spatiotemporal Resolution, Structure 19, 1064-1073 (2011).
  115. Balci, H., S. Arslan, S. Myong, T. M. Lohman and T. Ha, Single-Molecule Nanopositioning: Structural Transitions of a Helicase-DNA Complex during ATP Hydrolysis, Biophysical Journal 101, 976-984 (2011).
  116. Kim, H., G. Q. Tang, S. S. Patel and T. Ha, Opening–closing dynamics of the mitochondrial transcription pre-initiation complex, Nucleic Acids Research 40, 371-380 (2011).
  117. Ha T. and S. Myong, A single-molecule view of chaperonin cooperativity, Proc. Nat. Acad. Sci. USA, 108(41),16865-16866 (2011).
  118. Zhou, R., S. Kunzelmann, M.R. Webb and T. Ha, Detecting intramolecular conformational dynamics of single molecules in short distance range with sub-nanometer sensitivity, Nano Letters 11, 5482-5488 (2011).
  119. Means, C. K., B. Lygren, L. K. Langeberg, A. Jain, R. E. Dixon, A. L. Vega, M. G. Gold, S. Petrosyan, S. S. Taylor, A. N. Murphy, T. Ha, L. F. Santana, K. Tasken, and J. D. Scott, An entirely specific type I A-kinase anchoring protein that can sequester two molecules of protein kinase A at mitochondria, Proc. Nat. Acad. Sci. USA,108(48):E1227-35 (2011).
  120. Morrison, E. A., G. T. DeKoster, S. Dutta, R. Vafabakhsh, M. W. Clarkson, A. Bahl, D. Kern, T. Ha and K. A. Henzler-Wildman, Antiparallel EmrE exports drugs by exchanging between asymmetric structures, Nature 481, 45-50 (2012).
  121. Jain, A., R. Liu, Y.K. Xiang and T. Ha, Single-molecule pull-down for studying protein interactions, Nature Protocols 7, 445–452 (2012).
  122. Ha, T., A. G. Kozlov and T. M. Lohman, Single-Molecule Views of Protein Movement on Single-Stranded DNA, Ann. Rev. Biophys. 41, (2012).
  123. Ha T. and P. Tinnefeld, Photophysics of Fluorescent Probes for Single-Molecule Biophysics and Super-Resolution Imaging, Ann. Rev. Phys. Chem. 63, (2012).
  124. Shi, X., Y. Jung, L.J. Lin, C. Liu, C. Wu, I.K.O. Cann and T. Ha, Quantitative Fluorescent Labeling of Aldehyde-Tagged Proteins for Single-Molecule Imaging, Nature Methods 9, 499-503 (2012).
  125. Chou, Y. Y., R. Vafabakhsh, S. Doğanay, Q. Gao, T. Ha and P. Palese, One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis, PNAS, (2012)
  126. Gao, Q., Y. Y. Chou, S. Doganay, R. Vafabakhsh, T. Ha and P. Palese, The influenza A virus PB2, PA, NP and M segments play a pivotal role during genome packaging, J. Virology, doi: 10.1128/ JVI.00662-12 (2012).
  127. Diao, J. Y., Ishitsuka, H. Lee, C. Joo, Z. Su, S. Syed, Y.K. Shin, T.Y. Yoon and T. Ha, A single vesicle-vesicle fusion assay for in vitro studies of SNAREs and accessory proteins, Nature Protocols 7, 921-934 (2012).
  128. Chen, K., J. Eargle, J. Lai, H. Kim, S. Abeysirigunawardena, M. Mayerle, S. A. Woodson, T. Ha and Z. Luthey-Schulten, Assembly of the Five-Way Junction in the Ribosomal Small Subunit Using Hybrid MD-Go Simulations, J. Phys. Chem. B, (2012).
  129. Cisse, I. I., H. Kim and T. Ha, A rule of seven in Watson-Crick base-pairing of mismatched sequences, Nature Structural & Molecular Biology, doi:10.1038/nsmb.2294 (2012).
  130. Shen, Z., A.Chakraborty, A. Jain, S. Giri, T. Ha, K.V. Prasanth and S. G Prasanth, Dynamic association of ORCA with pre-RC components regulates DNA replication initiation, Mol. Cell. Bio., doi: 10.1128/MCB.00362-12 (2012).
  131. Lee, G. and T. Ha, Single-molecule imaging: A collagenase pauses before embarking on a killing spree, Current Biology 22 (12), R499-R501 (2012).
  132. Zhou, R. and T. Ha, Single-molecule Analysis of SSB Dynamics on Single-stranded DNA. Methods Mol. Biol., 922, 85-100 (2012).

updated: 6/13/2012