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 , DOI: 10.1021/bi901991 (2010)
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 , doi:10.1093/nar/gkp1249 (2010)
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 , DOI: 10.1021/cn900034p (2010)
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)
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. , (2009)
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, 940-943 (2009)
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)
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)
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)
Jena P., P Shirude, B. Okumus, K. Laxmi-Reddy, F. Godde, I. Huc, S. Balasubramanian and Taekjip Ha, "G-Quadruplex DNA Bound by a Synthetic Ligand is Highly Dynamic", J. Am. Chem. Soc. 131, 12522–12523 (2009) ( pdf )
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) ( pdf )
Sorokina M., H. R. Koh, S. S. Patel and T. Ha, "Fluoresecent Lifetime Trajectories of a Single Fluorophore Reveal Reaction Intermediates During Transcription Initiation", J Am Chem Soc 131, 9630–9631 (2009) ( pdf )
Ha, T., "Photonics: How nanocrystals lost their blink", Nature 459 (7247), 649-650 (2009) ( pdf )
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 J 28, 405-416 (2009) ( pdf )
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 ribosomes", PNAS 106, 2571-2576 (2009)
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 prime - triphosphate-dependent translocase on double-stranded RNA", Science 323, 1070-1074 (2009)
Heller, D., H. Jin, B. Martinez, D. Patel, B. Miller, T.-K. Yeung, P. Jena, C. Hobartner, T. Ha, S. Silverman, M. Strano, "Multimodal optical sensing and analyte specificity using single-walled carbon nanotubes", Nature Nanotechnology 4(2), 114-120 (2009) ( pdf )
Ishitsuka, Y. and T. Ha, "DNA nanotechnology: a nanomachine goes live", Nat Nanotechnol. 4 (5), 281-282 (2009)
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", PNAS 205 (51), 20274-20279 (2008) ( pdf )
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) ( pdf )
Iqbal, A., S. Arslan, B. Okumus, T. J. Wilson, G. Giraud, D. G. Norman, T. Ha and D. M.J. Lilley, "Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids", PNAS 105(32), 11176-11181 (2008) ( pdf )
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) ( pdf )
Yoon, T.Y., X. Lu, J. Diao, S. M. Lee, T. Ha and Y. K. Shin, "Complexin and Calcium stimulate SNARE-mediated membrane fusion", Nature Structural & Molecular Biology 15, 707-713 (2008) ( pdf )
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) ( pdf )
Cornish, P. V., D. N. Ermolenko, H. F. Noller and T. Ha, "Spontaneous Intersubunit Rotation in Single Ribosomes", Molecular Cell 30, 578-588 (2008) ( pdf )
Tang, G. Q., R. Roy, T. Ha and S. S. Patel, "Transcription Initiation in a Single-Subunit RNA Polymerase Proceeds through DNA Scrunching and Rotation of the N-Terminal Subdomains", Molecular Cell 30, 567-577 (2008) ( pdf )
Rasnik, I., Y. J. Yeong, S. A. McKinney, V. Rajagopal, S. S. Patel and T. Ha., "Branch migration enzyme as a Brownian ratchet.", EMBO J. 27, 1727–1735 (2008) ( pdf )
Roy, R., S. Hohng and T. Ha., "A practical guide to single-molecule FRET.", Nat. Methods 5, 507-516 (2008) ( pdf )
Joo, C., H. Balci, Y. Ishitsuka, C. Buranachai, and T. Ha , "Advances in Single-Molecule Fluorescence Methods for Molecular Biology", Ann. Rev. of Biochemistry 77, 51-76 (2008) ( pdf )
Selvin, P.R. and T. Ha, Editors, "Single Molecule Techniques: A Laboratory Manual", Cold Spring Harbor Laboratory Press ISBN 978-087969775-4, 507 pp (2008)
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)
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 3, 763-768 (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) ( pdf )
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) ( pdf )
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) ( pdf )
Ha, T., "Need for Speed: Mechanical Regulation of a Replicative Helicase", Cell 129(7), 1249-1250 (2007) ( pdf )
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) ( pdf )
Cisse, I., B. Okumus, C. Joo, T. Ha, "Fueling Protein-DNA Interactions Inside Porous Nanocontainers", PNAS 104, 12646-12650 (2007) ( pdf )
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) ( pdf )
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) ( pdf )
Cornish P. and T. Ha, "A Survey of Single Molecule Techniques in Chemical Biology", ACS Chemical Biology 2, 53-61 (2007) ( pdf )
Yoon, T., B. Okumus, F. Zhang, Y.K. Shin and T. Ha, "Multiple Intermediates in SNARE-induced Membrane Fusion", PNAS 103, 19731-19736 (2006) ( pdf )
Rasnik, I., S. A. McKinney, and T. Ha, "Nonblinking and Long-lasting Single Molecule Fluorescence Imaging", Nature Methods 3(11), 891-893 (2006) ( pdf )
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) ( pdf )
McKinney, S. A., C. Joo, and T. Ha, "Analysis of Single Molecule FRET Trajectories using Hidden Markov Modeling", Biophys. J. 91, 1941-1951 (2006) ( pdf )
Rasnik, I., S. Myong, and T. Ha, "Unraveling Helicase Mechanisms One Molecule at a Time", Nucl. Acids Res. 34, 4225-4231 (2006) ( pdf )
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) ( pdf )
Yu, J., T. Ha, and K. Schulten, "Structure-based Model of the Stepping Motor of PcrA Helicase", Biophys. J. 19, 2091-2114 (2006) ( pdf )
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) ( pdf )
Myong, S., B. Stevens, and T. Ha, "Bridging Conformational Dynamics and Function using Single-Molecule Spectroscopy", Structure 14, 633-643 (2006) ( pdf )
Buranachai, C., S. A. McKinney, and T. Ha, "Single Molecule Nanometronome", Nano Letters 102, 18938-18943 (2006) ( pdf )
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) ( pdf )
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) ( pdf )
Rasnik, I., S. A. McKinney, and T. Ha, "Surfaces and Orientations: Much to FRET about?", Accounts of Chemical Research 38, 542-548 (2005) ( pdf )
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", Biophys. J. 89, 413-417 (2005) ( pdf )
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. Nat. Acad. Sci. U.S.A. 102, 5715-5720 (2005) ( pdf )
Robbins, J.B., M. C. McKinney, C. E. Guzman, B. Sriratana, S. Fitz-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) ( pdf )
Hohng S. and T. Ha, "Single-molecule Quantum Dot Fluorescence Resonance Energy Transfer", ChemPhysChem 6(5), 956-960 (2005) ( pdf )
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", Chem. Biology 12, 217-218 (2005) ( pdf )
Yu, J., T. Ha, and K. Schulten, "Conformational Model of the Holliday Junction Transition Deduced from Molecular Dynamics Simulations", Nuc. Acids Res. 32(22), 6683-6695 (2004) ( pdf )
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(11), 1107-1113 (2004) ( pdf )
Okumus, B., T. J. Wilson, D. M. J. Lilley, and T. Ha, "Vesicle Encapsulation Studies Reveal that Single Molecule Ribozyme Heterogeneities are Intrinsic", Biophys. J. 87(4), 2798-2806 (2004) ( pdf )
Hohng, S., C. Joo, and T. Ha, "Single-Molecule Three-color FRET", Biophys. J. 87(2), 1328-1337 (2004) ( pdf )
Gordon, M. P., T. Ha, and P. R. Selvin, "Single Molecule High Resolution Imaging with Photobleaching", Proc. Natl. Acad. Sci. U.S.A. 101(17), 6462-6465 (2004) ( pdf )
Ha, T., "Structural Dynamics and Processing of Nucleic Acids Revealed by Single Molecule Spectroscopy", Biochemistry 43(14), 4055-4063 (2004) ( pdf )
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 Biol. 341(3), 739-751 (2004) ( pdf )
Hohng S. and T. Ha, "Near-complete Suppression of Quantum Dot Blinking in Ambient Conditions", J. Am. Chem. Soc. 126(5), 1324-1325 (2004) ( pdf )
Stevens, B. C. and T. Ha, "Discrete and Heterogeneous Rotational Dynamics of Single Membrane Probe Dyes in Gel Phase Supported Bilayers", J.of Chem. Physics 120(6), 2020-2029 (2004) ( pdf )
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 Mol. Biology 336(2), 395-408 (2004) ( pdf )
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. Mol. Biol. 336(1), 69-79 (2004) ( pdf )
McKinney, S. A., E. Tan, T. J. Wilson, M. K. Nahas, A. C. Declias, R. M. Clegg, D. M. J. Lilley, and T. Ha, "Single Molecule Studies of DNA and RNA Four-way Junctions", Biochem. Soc. Transactions 32, 41-45 (2004) ( pdf )
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 DNA Polymerase BI", J. Biol. Chem. 279(8), 6315-6326 (2004) ( pdf )
Murphy, M. C., I. Rasnik, W. Cheng, T. M. Lohman, and T. Ha, "Probing Single Stranded DNA Conformational Flexibility using Fluorescence Spectroscopy", Biophys. J. 86(4), 2530-2537 (2004) ( pdf )
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. U.S.A. 100(16), 9308 (2003) ( pdf )
Yildiz, A., 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(5628), 2061-2065 (2003) ( pdf )
Ha, T., and J. Xu, "Photodestruction Intermediates Probed by an Adjacent Reporter Molecule", Phys. Rev. Lett. 90(22), 223002 (1-4) (2003) ( pdf )
McKinney, S. A., A. C. Declais, D. M. J. Lilley, and T. Ha, "Structural Dynamics of Individual Holiday Junctions", Nature Structural Biology 10(2), 93-97 (2003) ( pdf )
Johnson, J. M., T. Ha, S. Chu, S. G. Boxer, "Early Steps of Supported Bilayer Formation Probed by Single Vesicle Fluorescence Assays", Biophys J. 419(6907), 3371-3379 (2002)
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 Echerichia Coli Rep Helicase", Nature 419(6907), 638-641 (2002) ( pdf )
