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Complete Publication List

2018
[247] Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study (B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kuhnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Gotz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hubner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Rocker, H. Sanabria, M. Schlierf, T. Schroder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wunsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, T. Hugel), Nat. Methods, volume 15, 2018. [bibtex] [pdf]
[246] Mimicking Co-Transcriptional RNA Folding Using a Superhelicase (B. Hua, S. Panja, Y. Wang, S. A. Woodson, T. Ha), J. Am. Chem. Soc., volume 140, 2018. [bibtex] [pdf]
[245] Toward Single-Cell Single-Molecule Pull-Down (X. Wang, S. Park, L. Zeng, A. Jain, T. Ha), Biophys. J., volume 115, 2018. [bibtex] [pdf]
[244] Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution (H. R. Koh, R. Roy, M. Sorokina, G. Q. Tang, D. Nandakumar, S. S. Patel, T. Ha), Mol. Cell, volume 70, 2018. [bibtex] [pdf]
[243] Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis (D. Singh, Y. Wang, J. Mallon, O. Yang, J. Fei, A. Poddar, D. Ceylan, S. Bailey, T. Ha), Nat. Struct. Mol. Biol., volume 25, 2018. [bibtex] [pdf]
[242] Understanding the Molecular Mechanisms of the CRISPR Toolbox Using Single Molecule Approaches (D. Singh, T. Ha), ACS Chem. Biol., volume 13, 2018. [bibtex] [pdf]
[241] Editorial Overview: Single-Molecule Approaches up to Difficult Challenges in Folding and Dynamics (Y. Zhang, T. Ha, S. Marqusee), J. Mol. Biol., volume 430, 2018. [bibtex] [pdf]
[240] TGFβ1 reinforces arterial aging in the vascular smooth muscle cell through a long-range regulation of the cytoskeletal stiffness (W. Zhu, B. C. Kim, M. Wang, J. Huang, A. Isak, N. M. Bexiga, R. Monticone, T. Ha, E. G. Lakatta, S. S. An), Sci Rep, volume 8, 2018. [bibtex] [pdf]
[239] Mechanism of polypurine tract primer generation by HIV-1 reverse transcriptase (M. Figiel, M. Krepl, S. Park, J. Pozna?ski, K. Skowronek, A. Go??b, T. Ha, J. ?poner, M. Nowotny), J. Biol. Chem., volume 293, 2018. [bibtex] [pdf]
[238] Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a) (D. Singh, J. Mallon, A. Poddar, Y. Wang, R. Tippana, O. Yang, S. Bailey, T. Ha), Proc. Natl. Acad. Sci. U.S.A., volume 115, 2018. [bibtex] [pdf]
[237] The Single-Molecule Centroid Localization Algorithm Improves the Accuracy of Fluorescence Binding Assays (B. Hua, Y. Wang, S. Park, K. Y. Han, D. Singh, J. H. Kim, W. Cheng, T. Ha), Biochemistry, volume 57, 2018. [bibtex] [pdf]
[236] Cdc42-dependent modulation of rigidity sensing and cell spreading in tumor repopulating cells (F. Chowdhury, S. Do?anay, B. J. Leslie, R. Singh, K. Amar, B. Talluri, S. Park, N. Wang, T. Ha), Biochem. Biophys. Res. Commun., volume 500, 2018. [bibtex] [pdf]
[235] Single-Molecule FRET Analysis of Replicative Helicases (S. J. Lee, S. Syed, T. Ha), Methods Mol. Biol., volume 1805, 2018. [bibtex] [pdf]
[234] Single-Molecule Studies of ssDNA-Binding Proteins Exchange (O. Yang, T. Ha), Meth. Enzymol., volume 600, 2018. [bibtex] [pdf]
2017
[233] Voltage-gated sodium channels assemble and gate as dimers (J. Clatot, M. Hoshi, X. Wan, H. Liu, A. Jain, K. Shinlapawittayatorn, C. Marionneau, E. Ficker, T. Ha, I. Deschenes), Nat Commun, volume 8, 2017. [bibtex] [pdf]
[232] Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution (J. Fei, M. Jadaliha, T. S. Harmon, I. T. S. Li, B. Hua, Q. Hao, A. S. Holehouse, M. Reyer, Q. Sun, S. M. Freier, R. V. Pappu, K. V. Prasanth, T. Ha), J. Cell. Sci., volume 130, 2017. [bibtex] [pdf]
[231] Single-cell analysis of early antiviral gene expression reveals a determinant of stochastic IFNB1 expression (S. Do?anay, M. Y. Lee, A. Baum, J. Peh, S. Y. Hwang, J. Y. Yoo, P. J. Hergenrother, A. Garcia-Sastre, S. Myong, T. Ha), Integr Biol (Camb), volume 9, 2017. [bibtex] [pdf]
[230] Metals induce transient folding and activation of the twister ribozyme (S. Panja, B. Hua, D. Zegarra, T. Ha, S. A. Woodson), Nat. Chem. Biol., volume 13, 2017. [bibtex] [pdf]
[229] Sphingolipids facilitate age asymmetry of membrane proteins in dividing yeast cells (P. Singh, S. K. Ramachandran, J. Zhu, B. C. Kim, D. Biswas, T. Ha, P. A. Iglesias, R. Li), Mol. Biol. Cell, volume 28, 2017. [bibtex] [pdf]
[228] Single-molecule imaging reveals the translocation and DNA looping dynamics of hepatitis C virus NS3 helicase (C. T. Lin, F. Tritschler, K. S. Lee, M. Gu, C. M. Rice, T. Ha), Protein Sci., volume 26, 2017. [bibtex] [pdf]
[227] A genetically encoded fluorescent tRNA is active in live-cell protein synthesis (I. Masuda, T. Igarashi, R. Sakaguchi, R. G. Nitharwal, R. Takase, K. Y. Han, B. J. Leslie, C. Liu, H. Gamper, T. Ha, S. Sanyal, Y. M. Hou), Nucleic Acids Res., volume 45, 2017. [bibtex] [pdf]
[226] Structural biology: Growth factor rattled out of its cage (T. Ha), Nature, volume 542, 2017. [bibtex] [pdf]
[225] Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes (S. C. Abeysirigunawardena, H. Kim, J. Lai, K. Ragunathan, M. C. Rappe, Z. Luthey-Schulten, T. Ha, S. A. Woodson), Nat Commun, volume 8, 2017. [bibtex] [pdf]
[224] Notch-Jagged complex structure implicates a catch bond in tuning ligand sensitivity (V. C. Luca, B. C. Kim, C. Ge, S. Kakuda, D. Wu, M. Roein-Peikar, R. S. Haltiwanger, C. Zhu, T. Ha, K. C. Garcia), Science, volume 355, 2017. [bibtex] [pdf]
[223] Flipping nanoscopy on its head (J. Xiao, T. Ha), Science, volume 355, 2017. [bibtex] [pdf]
[222] Mapping cell surface adhesion by rotation tracking and adhesion footprinting (I. T. Li, T. Ha, Y. R. Chemla), Sci Rep, volume 7, 2017. [bibtex] [pdf]
[221] Probing Single Helicase Dynamics on Long Nucleic Acids Through Fluorescence-Force Measurement (C. T. Lin, T. Ha), Methods Mol. Biol., volume 1486, 2017. [bibtex] [pdf]
2016
[220] Correction: Nanoscale mechanics guides cellular decision making (Z. Rahil, S. Pedron, X. Wang, T. Ha, B. Harley, D. Leckband), Integr Biol (Camb), volume 8, 2016. [bibtex] [pdf]
[219] Rupture force of cell adhesion ligand tethers modulates biological activities of a cell-laden hydrogel (M. K. Lee, J. Park, X. Wang, M. Roein-Peikar, E. Ko, E. Qin, J. Lee, T. Ha, H. Kong), Chem. Commun. (Camb.), volume 52, 2016. [bibtex] [pdf]
[218] A Chemical Controller of SNARE-Driven Membrane Fusion That Primes Vesicles for Ca(2+)-Triggered Millisecond Exocytosis (P. Heo, Y. Yang, K. Y. Han, B. Kong, J. H. Shin, Y. Jung, C. Jeong, J. Shin, Y. K. Shin, T. Ha, D. H. Kweon), J. Am. Chem. Soc., volume 138, 2016. [bibtex] [pdf]
[217] Natural antisense RNA promotes 3' end processing and maturation of MALAT1 lncRNA (X. Zong, S. Nakagawa, S. M. Freier, J. Fei, T. Ha, S. G. Prasanth, K. V. Prasanth), Nucleic Acids Res., volume 44, 2016. [bibtex] [pdf]
[216] Single-Molecule Analysis of Lipid-Protein Interactions in Crude Cell Lysates (E. Arauz, V. Aggarwal, A. Jain, T. Ha, J. Chen), Anal. Chem., volume 88, 2016. [bibtex] [pdf]
[215] Plantazolicin is an ultra-narrow spectrum antibiotic that targets the Bacillus anthracis membrane (K. J. Molohon, P. M. Blair, S. Park, J. R. Doroghazi, T. Maxson, J. R. Hershfield, K. M. Flatt, N. E. Schroeder, T. Ha, D. A. Mitchell), ACS Infect Dis, volume 2, 2016. [bibtex] [pdf]
[214] Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation (J. Yoo, H. Kim, A. Aksimentiev, T. Ha), Nat Commun, volume 7, 2016. [bibtex] [pdf]
[213] Probing Nature's Nanomachines One Molecule at a Time (T. Ha), Biophys. J., volume 110, 2016. [bibtex] [pdf]
[212] Spider Silk Peptide Is a Compact, Linear Nanospring Ideal for Intracellular Tension Sensing (M. D. Brenner, R. Zhou, D. E. Conway, L. Lanzano, E. Gratton, M. A. Schwartz, T. Ha), Nano Lett., volume 16, 2016. [bibtex] [pdf]
[211] Constructing modular and universal single molecule tension sensor using protein G to study mechano-sensitive receptors (X. Wang, Z. Rahil, I. T. Li, F. Chowdhury, D. E. Leckband, Y. R. Chemla, T. Ha), Sci Rep, volume 6, 2016. [bibtex] [pdf]
[210] Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability (T. T. Ngo, J. Yoo, Q. Dai, Q. Zhang, C. He, A. Aksimentiev, T. Ha), Nat Commun, volume 7, 2016. [bibtex] [pdf]
[209] The light side of the force (A. Basu, T. Ha), Elife, volume 5, 2016. [bibtex] [pdf]
[208] Structural dynamics of potassium-channel gating revealed by single-molecule FRET (S. Wang, R. Vafabakhsh, W. F. Borschel, T. Ha, C. G. Nichols), Nat. Struct. Mol. Biol., volume 23, 2016. [bibtex] [pdf]
[207] Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9 (D. Singh, S. H. Sternberg, J. Fei, J. A. Doudna, T. Ha), Nat Commun, volume 7, 2016. [bibtex] [pdf]
[206] Kaposi's Sarcoma-Associated Herpesvirus Viral Interferon Regulatory Factor 4 (vIRF4) Perturbs the G1-S Cell Cycle Progression via Deregulation of the cyclin D1 Gene (H. R. Lee, J. Mitra, S. Lee, S. J. Gao, T. K. Oh, M. H. Kim, T. Ha, J. U. Jung), J. Virol., volume 90, 2016. [bibtex] [pdf]
[205] Single-molecule fluorescence microscopy of native macromolecular complexes (V. Aggarwal, T. Ha), Curr. Opin. Struct. Biol., volume 41, 2016. [bibtex] [pdf]
[204] Nanoscale mechanics guides cellular decision making (Z. Rahil, S. Pedron, X. Wang, T. Ha, B. Harley, D. Leckband), Integr Biol (Camb), volume 8, 2016. [bibtex] [pdf]
[203] In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes (A. Y. Husbands, V. Aggarwal, T. Ha, M. C. Timmermans), Plant Cell, volume 28, 2016. [bibtex] [pdf]
[202] Defining Single Molecular Forces Required for Notch Activation Using Nano Yoyo (F. Chowdhury, I. T. Li, T. T. Ngo, B. J. Leslie, B. C. Kim, J. E. Sokoloski, E. Weiland, X. Wang, Y. R. Chemla, T. M. Lohman, T. Ha), Nano Lett., volume 16, 2016. [bibtex] [pdf]
[201] Ebola Virus Does Not Induce Stress Granule Formation during Infection and Sequesters Stress Granule Proteins within Viral Inclusions (E. V. Nelson, K. M. Schmidt, L. R. Deflube, S. Do?anay, L. Banadyga, J. Olejnik, A. J. Hume, E. Ryabchikova, H. Ebihara, N. Kedersha, T. Ha, E. Muhlberger), J. Virol., volume 90, 2016. [bibtex] [pdf]
2015
[200] Effects of DNA replication on mRNA noise (J. R. Peterson, J. A. Cole, J. Fei, T. Ha, Z. A. Luthey-Schulten), Proc. Natl. Acad. Sci. U.S.A., volume 112, 2015. [bibtex] [pdf]
[199] Integrin Molecular Tension within Motile Focal Adhesions (X. Wang, J. Sun, Q. Xu, F. Chowdhury, M. Roein-Peikar, Y. Wang, T. Ha), Biophys. J., volume 109, 2015. [bibtex] [pdf]
[198] Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells (J. Zhang, J. Fei, B. J. Leslie, K. Y. Han, T. E. Kuhlman, T. Ha), Sci Rep, volume 5, 2015. [bibtex] [pdf]
[197] Single molecular force across single integrins dictates cell spreading (F. Chowdhury, I. T. S. Li, B. J. Leslie, S. Do?anay, R. Singh, X. Wang, J. Seong, S. H. Lee, S. Park, N. Wang, T. Ha), Integr Biol (Camb), volume 7, 2015. [bibtex] [pdf]
[196] Allosteric Regulation of E-Cadherin Adhesion (N. Shashikanth, Y. I. Petrova, S. Park, J. Chekan, S. Maiden, M. Spano, T. Ha, B. M. Gumbiner, D. E. Leckband), J. Biol. Chem., volume 290, 2015. [bibtex] [pdf]
[195] BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase (A. Khan, S. Giri, Y. Wang, A. Chakraborty, A. K. Ghosh, A. Anantharaman, V. Aggarwal, K. M. Sathyan, T. Ha, K. V. Prasanth, S. G. Prasanth), Proc. Natl. Acad. Sci. U.S.A., volume 112, 2015. [bibtex] [pdf]
[194] Dual-color three-dimensional STED microscopy with a single high-repetition-rate laser (K. Y. Han, T. Ha), Opt Lett, volume 40, 2015. [bibtex] [pdf]
[193] A parameter estimation method for fluorescence lifetime data (D. Sewell, H. Kim, T. Ha, P. Ma), BMC Res Notes, volume 8, 2015. [bibtex] [pdf]
[192] Protein structure. Direct observation of structure-function relationship in a nucleic acid-processing enzyme (M. J. Comstock, K. D. Whitley, H. Jia, J. Sokoloski, T. M. Lohman, T. Ha, Y. R. Chemla), Science, volume 348, 2015. [bibtex] [pdf]
[191] Protein structure. Engineering of a superhelicase through conformational control (S. Arslan, R. Khafizov, C. D. Thomas, Y. R. Chemla, T. Ha), Science, volume 348, 2015. [bibtex] [pdf]
[190] The preRC protein ORCA organizes heterochromatin by assembling histone H3 lysine 9 methyltransferases on chromatin (S. Giri, V. Aggarwal, J. Pontis, Z. Shen, A. Chakraborty, A. Khan, C. Mizzen, K. V. Prasanth, S. Ait-Si-Ali, T. Ha, S. G. Prasanth), Elife, volume 4, 2015. [bibtex] [pdf]
[189] Nucleosomes undergo slow spontaneous gaping (T. T. Ngo, T. Ha), Nucleic Acids Res., volume 43, 2015. [bibtex] [pdf]
[188] RNA biochemistry. Determination of in vivo target search kinetics of regulatory noncoding RNA (J. Fei, D. Singh, Q. Zhang, S. Park, D. Balasubramanian, I. Golding, C. K. Vanderpool, T. Ha), Science, volume 347, 2015. [bibtex] [pdf]
[187] Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility (T. T. Ngo, Q. Zhang, R. Zhou, J. G. Yodh, T. Ha), Cell, volume 160, 2015. [bibtex] [pdf]
[186] Distinct mechanisms regulating mechanical force-induced Ca²⁺ signals at the plasma membrane and the ER in human MSCs (T. J. Kim, C. Joo, J. Seong, R. Vafabakhsh, E. L. Botvinick, M. W. Berns, A. E. Palmer, N. Wang, T. Ha, E. Jakobsson, J. Sun, Y. Wang), Elife, volume 4, 2015. [bibtex] [pdf]
[185] Dynamic growth and shrinkage govern the pH dependence of RecA filament stability (S. H. Kim, J. Park, C. Joo, D. Kim, T. Ha), PLoS ONE, volume 10, 2015. [bibtex] [pdf]
[184] RNA fluorescence in situ hybridization in cultured mammalian cells (V. Tripathi, J. Fei, T. Ha, K. V. Prasanth), Methods Mol. Biol., volume 1206, 2015. [bibtex] [pdf]
2014
[183] An improved surface passivation method for single-molecule studies (B. Hua, K. Y. Han, R. Zhou, H. Kim, X. Shi, S. C. Abeysirigunawardena, A. Jain, D. Singh, V. Aggarwal, S. A. Woodson, T. Ha), Nat. Methods, volume 11, 2014. [bibtex] [pdf]
[182] A price to pay for relaxed substrate specificity: a comparative kinetic analysis of the class II lanthipeptide synthetases ProcM and HalM2 (C. J. Thibodeaux, T. Ha, W. A. van der Donk), J. Am. Chem. Soc., volume 136, 2014. [bibtex] [pdf]
[181] Stoichiometry and assembly of mTOR complexes revealed by single-molecule pulldown (A. Jain, E. Arauz, V. Aggarwal, N. Ikon, J. Chen, T. Ha), Proc. Natl. Acad. Sci. U.S.A., volume 111, 2014. [bibtex] [pdf]
[180] Designing a nine cysteine-less DNA packaging motor from bacteriophage T4 reveals new insights into ATPase structure and function (K. Kondabagil, L. Dai, R. Vafabakhsh, T. Ha, B. Draper, V. B. Rao), Virology, volume 468-470, 2014. [bibtex] [pdf]
[179] Single-molecule pull-down (SiMPull) for new-age biochemistry: methodology and biochemical applications of single-molecule pull-down (SiMPull) for probing biomolecular interactions in crude cell extracts (V. Aggarwal, T. Ha), Bioessays, volume 36, 2014. [bibtex] [pdf]
[178] Targeting DNA G-quadruplexes with helical small molecules (S. Muller, K. Laxmi-Reddy, P. V. Jena, B. Baptiste, Z. Dong, F. Godde, T. Ha, R. Rodriguez, S. Balasubramanian, I. Huc), Chembiochem, volume 15, 2014. [bibtex] [pdf]
[177] Single-molecule methods leap ahead (T. Ha), Nat. Methods, volume 11, 2014. [bibtex] [pdf]
[176] Cooperative conformational transitions keep RecA filament active during ATPase cycle (S. H. Kim, K. Ragunathan, J. Park, C. Joo, D. Kim, T. Ha), J. Am. Chem. Soc., volume 136, 2014. [bibtex] [pdf]
[175] Single-molecule packaging initiation in real time by a viral DNA packaging machine from bacteriophage T4 (R. Vafabakhsh, K. Kondabagil, T. Earnest, K. S. Lee, Z. Zhang, L. Dai, K. A. Dahmen, V. B. Rao, T. Ha), Proc. Natl. Acad. Sci. U.S.A., volume 111, 2014. [bibtex] [pdf]
[174] A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment (C. Maffeo, T. T. Ngo, T. Ha, A. Aksimentiev), J Chem Theory Comput, volume 10, 2014. [bibtex] [pdf]
[173] Matrix softness regulates plasticity of tumour-repopulating cells via H3K9 demethylation and Sox2 expression (Y. Tan, A. Tajik, J. Chen, Q. Jia, F. Chowdhury, L. Wang, J. Chen, S. Zhang, Y. Hong, H. Yi, D. C. Wu, Y. Zhang, F. Wei, Y. C. Poh, J. Seong, R. Singh, L. J. Lin, S. Do?anay, Y. Li, H. Jia, T. Ha, Y. Wang, B. Huang, N. Wang), Nat Commun, volume 5, 2014. [bibtex] [pdf]
[172] Biophysics. Ultraslow relaxation of confined DNA (Y. R. Chemla, T. Ha), Science, volume 345, 2014. [bibtex] [pdf]
[171] Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer (K. S. Lee, A. B. Marciel, A. G. Kozlov, C. M. Schroeder, T. M. Lohman, T. Ha), J. Mol. Biol., volume 426, 2014. [bibtex] [pdf]
[170] Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA (R. Zhou, J. Zhang, M. L. Bochman, V. A. Zakian, T. Ha), Elife, volume 3, 2014. [bibtex] [pdf]
[169] Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA (J. Zhang, R. Zhou, J. Inoue, T. Mikawa, T. Ha), Nucleic Acids Res., volume 42, 2014. [bibtex] [pdf]
[168] Dynamic look at DNA unwinding by a replicative helicase (S. J. Lee, S. Syed, E. J. Enemark, S. Schuck, A. Stenlund, T. Ha, L. Joshua-Tor), Proc. Natl. Acad. Sci. U.S.A., volume 111, 2014. [bibtex] [pdf]
[167] Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase (S. Syed, M. Pandey, S. S. Patel, T. Ha), Cell Rep, volume 6, 2014. [bibtex] [pdf]
[166] Kaposi's sarcoma-associated herpesvirus viral interferon regulatory factor 4 (vIRF4) targets expression of cellular IRF4 and the Myc gene to facilitate lytic replication (H. R. Lee, S. Do?anay, B. Chung, Z. Toth, K. Brulois, S. Lee, Z. Kanketayeva, P. Feng, T. Ha, J. U. Jung), J. Virol., volume 88, 2014. [bibtex] [pdf]
[165] Crosstalk between the cGAS DNA sensor and Beclin-1 autophagy protein shapes innate antimicrobial immune responses (Q. Liang, G. J. Seo, Y. J. Choi, M. J. Kwak, J. Ge, M. A. Rodgers, M. Shi, B. J. Leslie, K. P. Hopfner, T. Ha, B. H. Oh, J. U. Jung), Cell Host Microbe, volume 15, 2014. [bibtex] [pdf]
[164] Protein-guided RNA dynamics during early ribosome assembly (H. Kim, S. C. Abeysirigunawarden, K. Chen, M. Mayerle, K. Ragunathan, Z. Luthey-Schulten, T. Ha, S. A. Woodson), Nature, volume 506, 2014. [bibtex] [pdf]
[163] Single-molecule optical spectroscopy (M. Orrit, T. Ha, V. Sandoghdar), Chem Soc Rev, volume 43, 2014. [bibtex] [pdf]
[162] Structural mechanisms of PriA-mediated DNA replication restart (B. Bhattacharyya, N. P. George, T. M. Thurmes, R. Zhou, N. Jani, S. R. Wessel, S. J. Sandler, T. Ha, J. L. Keck), Proc. Natl. Acad. Sci. U.S.A., volume 111, 2014. [bibtex] [pdf]
[161] Towards a computational model of a methane producing archaeum (J. R. Peterson, P. Labhsetwar, J. R. Ellermeier, P. R. Kohler, A. Jain, T. Ha, W. W. Metcalf, Z. Luthey-Schulten), Archaea, volume 2014, 2014. [bibtex] [pdf]
[160] Relaxed rotational and scrunching changes in P266L mutant of T7 RNA polymerase reduce short abortive RNAs while delaying transition into elongation (G. Q. Tang, D. Nandakumar, R. P. Bandwar, K. S. Lee, R. Roy, T. Ha, S. S. Patel), PLoS ONE, volume 9, 2014. [bibtex] [pdf]
2013
[159] Understanding the photophysics of the spinach-DFHBI RNA aptamer-fluorogen complex to improve live-cell RNA imaging (K. Y. Han, B. J. Leslie, J. Fei, J. Zhang, T. Ha), J. Am. Chem. Soc., volume 135, 2013. [bibtex] [pdf]
[158] Watching DNA breath one molecule at a time (J. Fei, T. Ha), Proc. Natl. Acad. Sci. U.S.A., volume 110, 2013. [bibtex] [pdf]
[157] Molecular mechanism of sequence-dependent stability of RecA filament (S. H. Kim, C. Joo, T. Ha, D. Kim), Nucleic Acids Res., volume 41, 2013. [bibtex] [pdf]
[156] ATPase-driven oligomerization of RIG-I on RNA allows optimal activation of type-I interferon (J. R. Patel, A. Jain, Y. Y. Chou, A. Baum, T. Ha, A. Garcia-Sastre), EMBO Rep., volume 14, 2013. [bibtex] [pdf]
[155] Single-molecule approaches embrace molecular cohorts (T. Ha), Cell, volume 154, 2013. [bibtex] [pdf]
[154] A dendritic single-molecule fluorescent probe that is monovalent, photostable and minimally blinking (S. K. Yang, X. Shi, S. Park, T. Ha, S. C. Zimmerman), Nat Chem, volume 5, 2013. [bibtex] [pdf]
[153] Single-molecule FRET reveals the native-state dynamics of the IκBα ankyrin repeat domain (J. A. Lamboy, H. Kim, H. Dembinski, T. Ha, E. A. Komives), J. Mol. Biol., volume 425, 2013. [bibtex] [pdf]
[152] PriC-mediated DNA replication restart requires PriC complex formation with the single-stranded DNA-binding protein (S. R. Wessel, A. H. Marceau, S. C. Massoni, R. Zhou, T. Ha, S. J. Sandler, J. L. Keck), J. Biol. Chem., volume 288, 2013. [bibtex] [pdf]
[151] Defining single molecular forces required to activate integrin and notch signaling (X. Wang, T. Ha), Science, volume 340, 2013. [bibtex] [pdf]
[150] Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation (D. N. Ermolenko, P. V. Cornish, T. Ha, H. F. Noller), RNA, volume 19, 2013. [bibtex] [pdf]
[149] The SOSS1 single-stranded DNA binding complex promotes DNA end resection in concert with Exo1 (S. H. Yang, R. Zhou, J. Campbell, J. Chen, T. Ha, T. T. Paull), EMBO J., volume 32, 2013. [bibtex] [pdf]
[148] Fusion pore formation and expansion induced by Ca2+ and synaptotagmin 1 (Y. Lai, J. Diao, Y. Liu, Y. Ishitsuka, Z. Su, K. Schulten, T. Ha, Y. K. Shin), Proc. Natl. Acad. Sci. U.S.A., volume 110, 2013. [bibtex] [pdf]
[147] Single-molecule nanometry for biological physics (H. Kim, T. Ha), Rep Prog Phys, volume 76, 2013. [bibtex] [pdf]
[146] Direct imaging of single UvrD helicase dynamics on long single-stranded DNA (K. S. Lee, H. Balci, H. Jia, T. M. Lohman, T. Ha), Nat Commun, volume 4, 2013. [bibtex] [pdf]
[145] The telomere capping complex CST has an unusual stoichiometry, makes multipartite interaction with G-Tails, and unfolds higher-order G-tail structures (N. F. Lue, R. Zhou, L. Chico, N. Mao, O. Steinberg-Neifach, T. Ha), PLoS Genet., volume 9, 2013. [bibtex] [pdf]
2012
[144] Activated GTPase movement on an RNA scaffold drives co-translational protein targeting (K. Shen, S. Arslan, D. Akopian, T. Ha, S. O. Shan), Nature, volume 492, 2012. [bibtex] [pdf]
[143] Single-molecule FRET with total internal reflection microscopy (C. Joo, T. Ha), Cold Spring Harb Protoc, volume 2012, 2012. [bibtex] [pdf]
[142] Prism-type total internal reflection microscopy for single-molecule FRET (C. Joo, T. Ha), Cold Spring Harb Protoc, volume 2012, 2012. [bibtex] [pdf]
[141] RecA filament sliding on DNA facilitates homology search (K. Ragunathan, C. Liu, T. Ha), Elife, volume 1, 2012. [bibtex] [pdf]
[140] Objective-type total internal reflection microscopy (excitation) for single-molecule FRET (C. Joo, T. Ha), Cold Spring Harb Protoc, volume 2012, 2012. [bibtex] [pdf]
[139] Objective-type total internal reflection microscopy (emission) for single-molecule FRET (C. Joo, T. Ha), Cold Spring Harb Protoc, volume 2012, 2012. [bibtex] [pdf]
[138] Imaging and identifying impurities in single-molecule FRET studies (C. Joo, T. Ha), Cold Spring Harb Protoc, volume 2012, 2012. [bibtex] [pdf]
[137] A helicase with an extra spring in its step (M. Schlierf, T. Ha), Cell, volume 151, 2012. [bibtex] [pdf]
[136] Preparing sample chambers for single-molecule FRET (C. Joo, T. Ha), Cold Spring Harb Protoc, volume 2012, 2012. [bibtex] [pdf]
[135] Dynamics of major histocompatibility complex class I association with the human peptide-loading complex (M. S. Panter, A. Jain, R. M. Leonhardt, T. Ha, P. Cresswell), J. Biol. Chem., volume 287, 2012. [bibtex] [pdf]
[134] Labeling proteins for single-molecule FRET (C. Joo, T. Ha), Cold Spring Harb Protoc, volume 2012, 2012. [bibtex] [pdf]
[133] Labeling DNA (or RNA) for single-molecule FRET (C. Joo, T. Ha), Cold Spring Harb Protoc, volume 2012, 2012. [bibtex] [pdf]
[132] Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization (R. Vafabakhsh, T. Ha), Science, volume 337, 2012. [bibtex] [pdf]
[131] Dynamic association of ORCA with prereplicative complex components regulates DNA replication initiation (Z. Shen, A. Chakraborty, A. Jain, S. Giri, T. Ha, K. V. Prasanth, S. G. Prasanth), Mol. Cell. Biol., volume 32, 2012. [bibtex] [pdf]
[130] The influenza A virus PB2, PA, NP, and M segments play a pivotal role during genome packaging (Q. Gao, Y. Y. Chou, S. Do?anay, R. Vafabakhsh, T. Ha, P. Palese), J. Virol., volume 86, 2012. [bibtex] [pdf]
[129] One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis (Y. Y. Chou, R. Vafabakhsh, S. Do?anay, Q. Gao, T. Ha, P. Palese), Proc. Natl. Acad. Sci. U.S.A., volume 109, 2012. [bibtex] [pdf]
[128] Elastic coupling between RNA degradation and unwinding by an exoribonuclease (G. Lee, M. A. Bratkowski, F. Ding, A. Ke, T. Ha), Science, volume 336, 2012. [bibtex] [pdf]
[127] Single-molecule imaging: a collagenase pauses before embarking on a killing spree (G. Lee, T. Ha), Curr. Biol., volume 22, 2012. [bibtex] [pdf]
[126] Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulations (K. Chen, J. Eargle, J. Lai, H. Kim, S. Abeysirigunawardena, M. Mayerle, S. Woodson, T. Ha, Z. Luthey-Schulten), J Phys Chem B, volume 116, 2012. [bibtex] [pdf]
[125] A rule of seven in Watson-Crick base-pairing of mismatched sequences (I. I. Cisse, H. Kim, T. Ha), Nat. Struct. Mol. Biol., volume 19, 2012. [bibtex] [pdf]
[124] A single vesicle-vesicle fusion assay for in vitro studies of SNAREs and accessory proteins (J. Diao, Y. Ishitsuka, H. Lee, C. Joo, Z. Su, S. Syed, Y. K. Shin, T. Y. Yoon, T. Ha), Nat Protoc, volume 7, 2012. [bibtex] [pdf]
[123] Quantitative fluorescence labeling of aldehyde-tagged proteins for single-molecule imaging (X. Shi, Y. Jung, L. J. Lin, C. Liu, C. Wu, I. K. Cann, T. Ha), Nat. Methods, volume 9, 2012. [bibtex] [pdf]
[122] Single-molecule pull-down for studying protein interactions (A. Jain, R. Liu, Y. K. Xiang, T. Ha), Nat Protoc, volume 7, 2012. [bibtex] [pdf]
[121] Opening-closing dynamics of the mitochondrial transcription pre-initiation complex (H. Kim, G. Q. Tang, S. S. Patel, T. Ha), Nucleic Acids Res., volume 40, 2012. [bibtex] [pdf]
[120] Single-molecule analysis of SSB dynamics on single-stranded DNA (R. Zhou, T. Ha), Methods Mol. Biol., volume 922, 2012. [bibtex] [pdf]
[119] Single-molecule views of protein movement on single-stranded DNA (T. Ha, A. G. Kozlov, T. M. Lohman), Annu Rev Biophys, volume 41, 2012. [bibtex] [pdf]
[118] Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging (T. Ha, P. Tinnefeld), Annu Rev Phys Chem, volume 63, 2012. [bibtex] [pdf]
2011
[117] Detecting intramolecular conformational dynamics of single molecules in short distance range with subnanometer sensitivity (R. Zhou, S. Kunzelmann, M. R. Webb, T. Ha), Nano Lett., volume 11, 2011. [bibtex] [pdf]
[116] Antiparallel EmrE exports drugs by exchanging between asymmetric structures (E. A. Morrison, G. T. DeKoster, S. Dutta, R. Vafabakhsh, M. W. Clarkson, A. Bahl, D. Kern, T. Ha, K. A. Henzler-Wildman), Nature, volume 481, 2011. [bibtex] [pdf]
[115] An entirely specific type I A-kinase anchoring protein that can sequester two molecules of protein kinase A at mitochondria (C. K. Means, 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, J. D. Scott), Proc. Natl. Acad. Sci. U.S.A., volume 108, 2011. [bibtex] [pdf]
[114] A single-molecule view of chaperonin cooperativity (T. Ha, S. Myong), Proc. Natl. Acad. Sci. U.S.A., volume 108, 2011. [bibtex] [pdf]
[113] Real-time observation of strand exchange reaction with high spatiotemporal resolution (K. Ragunathan, C. Joo, T. Ha), Structure, volume 19, 2011. [bibtex] [pdf]
[112] Single-molecule nanopositioning: structural transitions of a helicase-DNA complex during ATP hydrolysis (H. Balci, S. Arslan, S. Myong, T. M. Lohman, T. Ha), Biophys. J., volume 101, 2011. [bibtex] [pdf]
[111] Rotations of the 2B sub-domain of E. coli UvrD helicase/translocase coupled to nucleotide and DNA binding (H. Jia, S. Korolev, A. Niedziela-Majka, N. K. Maluf, G. H. Gauss, S. Myong, T. Ha, G. Waksman, T. M. Lohman), J. Mol. Biol., volume 411, 2011. [bibtex] [pdf]
[110] Tyrosine phosphorylation enhances RAD52-mediated annealing by modulating its DNA binding (M. Honda, Y. Okuno, J. Yoo, T. Ha, M. Spies), EMBO J., volume 30, 2011. [bibtex] [pdf]
[109] Monovalent, clickable, uncharged, water-soluble perylenediimide-cored dendrimers for target-specific fluorescent biolabeling (S. K. Yang, X. Shi, S. Park, S. Doganay, T. Ha, S. C. Zimmerman), J. Am. Chem. Soc., volume 133, 2011. [bibtex] [pdf]
[108] SSB functions as a sliding platform that migrates on DNA via reptation (R. Zhou, A. G. Kozlov, R. Roy, J. Zhang, S. Korolev, T. M. Lohman, T. Ha), Cell, volume 146, 2011. [bibtex] [pdf]
[107] Editorial on nanobiology (S. K. Kim, T. Ha, J. P. Schermann), Phys Chem Chem Phys, volume 13, 2011. [bibtex] [pdf]
[106] Single-molecule analysis reveals three phases of DNA degradation by an exonuclease (G. Lee, J. Yoo, B. J. Leslie, T. Ha), Nat. Chem. Biol., volume 7, 2011. [bibtex] [pdf]
[105] Visualization of the nanospring dynamics of the IkappaBalpha ankyrin repeat domain in real time (J. A. Lamboy, H. Kim, K. S. Lee, T. Ha, E. A. Komives), Proc. Natl. Acad. Sci. U.S.A., volume 108, 2011. [bibtex] [pdf]
[104] Forcing a connection: impacts of single-molecule force spectroscopy on in vivo tension sensing (M. D. Brenner, R. Zhou, T. Ha), Biopolymers, volume 95, 2011. [bibtex] [pdf]
[103] Probing cellular protein complexes using single-molecule pull-down (A. Jain, R. Liu, B. Ramani, E. Arauz, Y. Ishitsuka, K. Ragunathan, J. Park, J. Chen, Y. K. Xiang, T. Ha), Nature, volume 473, 2011. [bibtex] [pdf]
[102] Ultrahigh-resolution optical trap with single-fluorophore sensitivity (M. J. Comstock, T. Ha, Y. R. Chemla), Nat. Methods, volume 8, 2011. [bibtex] [pdf]
[101] Seeing a molecular machine self-renew (X. Shi, T. Ha), Proc. Natl. Acad. Sci. U.S.A., volume 108, 2011. [bibtex] [pdf]
[100] Reverse-chaperoning activity of an AAA+ protein (C. Liu, M. C. McKinney, Y. H. Chen, T. M. Earnest, X. Shi, L. J. Lin, Y. Ishino, K. Dahmen, I. K. Cann, T. Ha), Biophys. J., volume 100, 2011. [bibtex] [pdf]
[99] A promiscuous DNA packaging machine from bacteriophage T4 (Z. Zhang, V. I. Kottadiel, R. Vafabakhsh, L. Dai, Y. R. Chemla, T. Ha, V. B. Rao), PLoS Biol., volume 9, 2011. [bibtex] [pdf]
[98] Homochirality and the origin of life. Editorial of the PCCP themed issue (S. K. Kim, T. Ha, J. P. Schermann), Phys Chem Chem Phys, volume 13, 2011. [bibtex] [pdf]
2010
[97] Temperature-independent porous nanocontainers for single-molecule fluorescence studies (Y. Ishitsuka, B. Okumus, S. Arslan, K. H. Chen, T. Ha), Anal. Chem., volume 82, 2010. [bibtex] [pdf]
[96] Reversible and controllable nanolocomotion of an RNA-processing machinery (G. Lee, S. Hartung, K. P. Hopfner, T. Ha), Nano Lett., volume 10, 2010. [bibtex] [pdf]
[95] Single-molecule four-color FRET (J. Lee, S. Lee, K. Ragunathan, C. Joo, T. Ha, S. Hohng), Angew. Chem. Int. Ed. Engl., volume 49, 2010. [bibtex] [pdf]
[94] 5'-Single-stranded/duplex DNA junctions are loading sites for E. coli UvrD translocase (E. J. Tomko, H. Jia, J. Park, N. K. Maluf, T. Ha, T. M. Lohman), EMBO J., volume 29, 2010. [bibtex] [pdf]
[93] Advances in mass spectrometry for biological science (S. K. Kim, T. Ha, J. P. Schermann), Phys Chem Chem Phys, volume 12, 2010. [bibtex] [pdf]
[92] The role of L1 stalk-tRNA interaction in the ribosome elongation cycle (L. G. Trabuco, E. Schreiner, J. Eargle, P. Cornish, T. Ha, Z. Luthey-Schulten, K. Schulten), J. Mol. Biol., volume 402, 2010. [bibtex] [pdf]
[91] Water in biological systems (S. K. Kim, T. Ha, J. P. Schermann), Phys Chem Chem Phys, volume 12, 2010. [bibtex] [pdf]
[90] A single-vesicle content mixing assay for SNARE-mediated membrane fusion (J. Diao, Z. Su, Y. Ishitsuka, B. Lu, K. S. Lee, Y. Lai, Y. K. Shin, T. Ha), Nat Commun, volume 1, 2010. [bibtex] [pdf]
[89] PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps (J. Park, S. Myong, A. Niedziela-Majka, K. S. Lee, J. Yu, T. M. Lohman, T. Ha), Cell, volume 142, 2010. [bibtex] [pdf]
[88] Acidification of the oxygen scavenging system in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe (X. Shi, J. Lim, T. Ha), Anal. Chem., volume 82, 2010. [bibtex] [pdf]
[87] Measuring mechanical tension across vinculin reveals regulation of focal adhesion dynamics (C. Grashoff, B. D. Hoffman, M. D. Brenner, R. Zhou, M. Parsons, M. T. Yang, M. A. McLean, S. G. Sligar, C. S. Chen, T. Ha, M. A. Schwartz), Nature, volume 466, 2010. [bibtex] [pdf]
[86] Human Rad52 binds and wraps single-stranded DNA and mediates annealing via two hRad52-ssDNA complexes (J. M. Grimme, M. Honda, R. Wright, Y. Okuno, E. Rothenberg, A. V. Mazin, T. Ha, M. Spies), Nucleic Acids Res., volume 38, 2010. [bibtex] [pdf]
[85] Inching over hurdles: how DNA helicases move on crowded lattices (M. Spies, T. Ha), Cell Cycle, volume 9, 2010. [bibtex] [pdf]
[84] Insight into helicase mechanism and function revealed through single-molecule approaches (J. G. Yodh, M. Schlierf, T. Ha), Q. Rev. Biophys., volume 43, 2010. [bibtex] [pdf]
[83] Biomolecular structures: from isolated molecules to the cell crowded medium (S. K. Kim, T. Ha, J. P. Schermann), Phys Chem Chem Phys, volume 12, 2010. [bibtex] [pdf]
[82] A comparative study of multivariate and univariate hidden Markov modelings in time-binned single-molecule FRET data analysis (Y. Liu, J. Park, K. A. Dahmen, Y. R. Chemla, T. Ha), J Phys Chem B, volume 114, 2010. [bibtex] [pdf]
[81] Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine (M. D. Brenner, M. S. Scanlan, M. K. Nahas, T. Ha, S. K. Silverman), Biochemistry, volume 49, 2010. [bibtex] [pdf]
[80] Single-Vesicle Fusion Assay Reveals Munc18-1 Binding to the SNARE Core Is Sufficient for Stimulating Membrane Fusion (J. Diao, Z. Su, X. Lu, T. Y. Yoon, Y. K. Shin, T. Ha), ACS Chem Neurosci, volume 1, 2010. [bibtex] [pdf]
[79] Stepwise translocation of nucleic acid motors (S. Myong, T. Ha), Curr. Opin. Struct. Biol., volume 20, 2010. [bibtex] [pdf]
[78] Force-fluorescence spectroscopy at the single-molecule level (R. Zhou, M. Schlierf, T. Ha), Meth. Enzymol., volume 475, 2010. [bibtex] [pdf]
[77] Single-molecule FRET analysis of helicase functions (E. Rothenberg, T. Ha), Methods Mol. Biol., volume 587, 2010. [bibtex] [pdf]
[76] Real-time observation of G-quadruplex dynamics using single-molecule FRET microscopy (B. Okumus, T. Ha), Methods Mol. Biol., volume 608, 2010. [bibtex] [pdf]
2009
[75] Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase (G. Q. Tang, R. Roy, R. P. Bandwar, T. Ha, S. S. Patel), Proc. Natl. Acad. Sci. U.S.A., volume 106, 2009. [bibtex] [pdf]
[74] Coordinating DNA replication by means of priming loop and differential synthesis rate (M. Pandey, S. Syed, I. Donmez, G. Patel, T. Ha, S. S. Patel), Nature, volume 462, 2009. [bibtex] [pdf]
[73] SSB protein diffusion on single-stranded DNA stimulates RecA filament formation (R. Roy, A. G. Kozlov, T. M. Lohman, T. Ha), Nature, volume 461, 2009. [bibtex] [pdf]
[72] Single molecule nanocontainers made porous using a bacterial toxin (B. Okumus, S. Arslan, S. M. Fengler, S. Myong, T. Ha), J. Am. Chem. Soc., volume 131, 2009. [bibtex] [pdf]
[71] G-quadruplex DNA bound by a synthetic ligand is highly dynamic (P. V. Jena, P. S. Shirude, B. Okumus, K. Laxmi-Reddy, F. Godde, I. Huc, S. Balasubramanian, T. Ha), J. Am. Chem. Soc., volume 131, 2009. [bibtex] [pdf]
[70] Single-molecule analysis reveals differential effect of ssDNA-binding proteins on DNA translocation by XPD helicase (M. Honda, J. Park, R. A. Pugh, T. Ha, M. Spies), Mol. Cell, volume 35, 2009. [bibtex] [pdf]
[69] Fluorescent lifetime trajectories of a single fluorophore reveal reaction intermediates during transcription initiation (M. Sorokina, H. R. Koh, S. S. Patel, T. Ha), J. Am. Chem. Soc., volume 131, 2009. [bibtex] [pdf]
[68] C2AB: a molecular glue for lipid vesicles with a negatively charged surface (J. Diao, T. Y. Yoon, Z. Su, Y. K. Shin, T. Ha), Langmuir, volume 25, 2009. [bibtex] [pdf]
[67] Photonics: How nanocrystals lost their blink (T. Ha), Nature, volume 459, 2009. [bibtex] [pdf]
[66] DNA nanotechnology: a nanomachine goes live (Y. Ishitsuka, T. Ha), Nat Nanotechnol, volume 4, 2009. [bibtex] [pdf]
[65] Multimodal optical sensing and analyte specificity using single-walled carbon nanotubes (D. A. Heller, H. Jin, B. M. Martinez, D. Patel, B. M. Miller, T. K. Yeung, P. V. Jena, C. Hobartner, T. Ha, S. K. Silverman, M. S. Strano), Nat Nanotechnol, volume 4, 2009. [bibtex] [pdf]
[64] BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiation (J. G. Yodh, B. C. Stevens, R. Kanagaraj, P. Janscak, T. Ha), EMBO J., volume 28, 2009. [bibtex] [pdf]
[63] Following movement of the L1 stalk between three functional states in single ribosomes (P. V. Cornish, D. N. Ermolenko, D. W. Staple, L. Hoang, R. P. Hickerson, H. F. Noller, T. Ha), Proc. Natl. Acad. Sci. U.S.A., volume 106, 2009. [bibtex] [pdf]
[62] Cytosolic viral sensor RIG-I is a 5'-triphosphate-dependent translocase on double-stranded RNA (S. Myong, S. Cui, P. V. Cornish, A. Kirchhofer, M. U. Gack, J. U. Jung, K. P. Hopfner, T. Ha), Science, volume 323, 2009. [bibtex] [pdf]
2008
[61] Human Rad52-mediated homology search and annealing occurs by continuous interactions between overlapping nucleoprotein complexes (E. Rothenberg, J. M. Grimme, M. Spies, T. Ha), Proc. Natl. Acad. Sci. U.S.A., volume 105, 2008. [bibtex] [pdf]
[60] Roles of RIG-I N-terminal tandem CARD and splice variant in TRIM25-mediated antiviral signal transduction (M. U. Gack, A. Kirchhofer, Y. C. Shin, K. S. Inn, C. Liang, S. Cui, S. Myong, T. Ha, K. P. Hopfner, J. U. Jung), Proc. Natl. Acad. Sci. U.S.A., volume 105, 2008. [bibtex] [pdf]
[59] Engineering of functional replication protein a homologs based on insights into the evolution of oligonucleotide/oligosaccharide-binding folds (Y. Lin, L. J. Lin, P. Sriratana, K. Coleman, T. Ha, M. Spies, I. K. Cann), J. Bacteriol., volume 190, 2008. [bibtex] [pdf]
[58] Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids (A. Iqbal, S. Arslan, B. Okumus, T. J. Wilson, G. Giraud, D. G. Norman, T. Ha, D. M. Lilley), Proc. Natl. Acad. Sci. U.S.A., volume 105, 2008. [bibtex] [pdf]
[57] The SNARE complex from yeast is partially unstructured on the membrane (Z. Su, Y. Ishitsuka, T. Ha, Y. K. Shin), Structure, volume 16, 2008. [bibtex] [pdf]
[56] Complexin and Ca2+ stimulate SNARE-mediated membrane fusion (T. Y. Yoon, X. Lu, J. Diao, S. M. Lee, T. Ha, Y. K. Shin), Nat. Struct. Mol. Biol., volume 15, 2008. [bibtex] [pdf]
[55] Transcription initiation in a single-subunit RNA polymerase proceeds through DNA scrunching and rotation of the N-terminal subdomains (G. Q. Tang, R. Roy, T. Ha, S. S. Patel), Mol. Cell, volume 30, 2008. [bibtex] [pdf]
[54] Branch migration enzyme as a Brownian ratchet (I. Rasnik, Y. J. Jeong, S. A. McKinney, V. Rajagopal, S. S. Patel, T. Ha), EMBO J., volume 27, 2008. [bibtex] [pdf]
[53] Spontaneous intersubunit rotation in single ribosomes (P. V. Cornish, D. N. Ermolenko, H. F. Noller, T. Ha), Mol. Cell, volume 30, 2008. [bibtex] [pdf]
[52] A practical guide to single-molecule FRET (R. Roy, S. Hohng, T. Ha), Nat. Methods, volume 5, 2008. [bibtex] [pdf]
[51] Advances in single-molecule fluorescence methods for molecular biology (C. Joo, H. Balci, Y. Ishitsuka, C. Buranachai, T. Ha), Annu. Rev. Biochem., volume 77, 2008. [bibtex] [pdf]
2007
[50] Dissecting metal ion-dependent folding and catalysis of a single DNAzyme (H. K. Kim, I. Rasnik, J. Liu, T. Ha, Y. Lu), Nat. Chem. Biol., volume 3, 2007. [bibtex] [pdf]
[49] How directional translocation is regulated in a DNA helicase motor (J. Yu, T. Ha, K. Schulten), Biophys. J., volume 93, 2007. [bibtex] [pdf]
[48] MCM forked substrate specificity involves dynamic interaction with the 5'-tail (E. Rothenberg, M. A. Trakselis, S. D. Bell, T. Ha), J. Biol. Chem., volume 282, 2007. [bibtex] [pdf]
[47] Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction (S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. Lilley, T. Ha), Science, volume 318, 2007. [bibtex] [pdf]
[46] Fueling protein DNA interactions inside porous nanocontainers (I. Cisse, B. Okumus, C. Joo, T. Ha), Proc. Natl. Acad. Sci. U.S.A., volume 104, 2007. [bibtex] [pdf]
[45] Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase (S. Myong, M. M. Bruno, A. M. Pyle, T. Ha), Science, volume 317, 2007. [bibtex] [pdf]
[44] Need for speed: mechanical regulation of a replicative helicase (T. Ha), Cell, volume 129, 2007. [bibtex] [pdf]
[43] Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein (R. Roy, A. G. Kozlov, T. M. Lohman, T. Ha), J. Mol. Biol., volume 369, 2007. [bibtex] [pdf]
[42] Single-molecule conformational analysis of G-quadruplex formation in the promoter DNA duplex of the proto-oncogene c-kit (P. S. Shirude, B. Okumus, L. Ying, T. Ha, S. Balasubramanian), J. Am. Chem. Soc., volume 129, 2007. [bibtex] [pdf]
[41] A survey of single-molecule techniques in chemical biology (P. V. Cornish, T. Ha), ACS Chem. Biol., volume 2, 2007. [bibtex] [pdf]
[40] Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA (V. Arluison, S. Hohng, R. Roy, O. Pellegrini, P. Regnier, T. Ha), Nucleic Acids Res., volume 35, 2007. [bibtex] [pdf]
[39] RNA folding and the origins of catalytic activity in the hairpin ribozyme (T. J. Wilson, M. Nahas, L. Araki, S. Harusawa, T. Ha, D. M. Lilley), Blood Cells Mol. Dis., volume 38, 2007. [bibtex] [pdf]
2006
[38] Multiple intermediates in SNARE-induced membrane fusion (T. Y. Yoon, B. Okumus, F. Zhang, Y. K. Shin, T. Ha), Proc. Natl. Acad. Sci. U.S.A., volume 103, 2006. [bibtex] [pdf]
[37] Nonblinking and long-lasting single-molecule fluorescence imaging (I. Rasnik, S. A. McKinney, T. Ha), Nat. Methods, volume 3, 2006. [bibtex] [pdf]
[36] Methanosarcina acetivorans flap endonuclease 1 activity is inhibited by a cognate single-stranded-DNA-binding protein (Y. Lin, C. E. Guzman, M. C. McKinney, S. K. Nair, T. Ha, I. K. Cann), J. Bacteriol., volume 188, 2006. [bibtex] [pdf]
[35] Structure-based model of the stepping motor of PcrA helicase (J. Yu, T. Ha, K. Schulten), Biophys. J., volume 91, 2006. [bibtex] [pdf]
[34] Analysis of single-molecule FRET trajectories using hidden Markov modeling (S. A. McKinney, C. Joo, T. Ha), Biophys. J., volume 91, 2006. [bibtex] [pdf]
[33] Real-time observation of RecA filament dynamics with single monomer resolution (C. Joo, S. A. McKinney, M. Nakamura, I. Rasnik, S. Myong, T. Ha), Cell, volume 126, 2006. [bibtex] [pdf]
[32] Bridging conformational dynamics and function using single-molecule spectroscopy (S. Myong, B. C. Stevens, T. Ha), Structure, volume 14, 2006. [bibtex] [pdf]
[31] Defocused orientation and position imaging (DOPI) of myosin V (E. Toprak, J. Enderlein, S. Syed, S. A. McKinney, R. G. Petschek, T. Ha, Y. E. Goldman, P. R. Selvin), Proc. Natl. Acad. Sci. U.S.A., volume 103, 2006. [bibtex] [pdf]
[30] Single molecule nanometronome (C. Buranachai, S. A. McKinney, T. Ha), Nano Lett., volume 6, 2006. [bibtex] [pdf]
[29] Unraveling helicase mechanisms one molecule at a time (I. Rasnik, S. Myong, T. Ha), Nucleic Acids Res., volume 34, 2006. [bibtex] [pdf]
2005
[28] Extreme conformational diversity in human telomeric DNA (J. Y. Lee, B. Okumus, D. S. Kim, T. Ha), Proc. Natl. Acad. Sci. U.S.A., volume 102, 2005. [bibtex] [pdf]
[27] Repetitive shuttling of a motor protein on DNA (S. Myong, I. Rasnik, C. Joo, T. M. Lohman, T. Ha), Nature, volume 437, 2005. [bibtex] [pdf]
[26] Interhead distance measurements in myosin VI via SHRImP support a simplified hand-over-hand model (H. Balci, T. Ha, H. L. Sweeney, P. R. Selvin), Biophys. J., volume 89, 2005. [bibtex] [pdf]
[25] Surfaces and orientations: much to FRET about? (I. Rasnik, S. A. McKinney, T. Ha), Acc. Chem. Res., volume 38, 2005. [bibtex] [pdf]
[24] Single-molecule quantum-dot fluorescence resonance energy transfer (S. Hohng, T. Ha), Chemphyschem, volume 6, 2005. [bibtex] [pdf]
[23] Observing spontaneous branch migration of Holliday junctions one step at a time (S. A. McKinney, A. D. Freeman, D. M. Lilley, T. Ha), Proc. Natl. Acad. Sci. U.S.A., volume 102, 2005. [bibtex] [pdf]
[22] The euryarchaeota, nature's medium for engineering of single-stranded DNA-binding proteins (J. B. Robbins, M. C. McKinney, C. E. Guzman, B. Sriratana, S. Fitz-Gibbon, T. Ha, I. K. Cann), J. Biol. Chem., volume 280, 2005. [bibtex] [pdf]
[21] Stereospecific effects determine the structure of a four-way DNA junction (J. Liu, A. C. Declais, S. A. McKinney, T. Ha, D. G. Norman, D. M. Lilley), Chem. Biol., volume 12, 2005. [bibtex] [pdf]
2004
[20] Observation of internal cleavage and ligation reactions of a ribozyme (M. K. Nahas, T. J. Wilson, S. Hohng, K. Jarvie, D. M. Lilley, T. Ha), Nat. Struct. Mol. Biol., volume 11, 2004. [bibtex] [pdf]
[19] Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic (B. Okumus, T. J. Wilson, D. M. Lilley, T. Ha), Biophys. J., volume 87, 2004. [bibtex] [pdf]
[18] Exploring rare conformational species and ionic effects in DNA Holliday junctions using single-molecule spectroscopy (C. Joo, S. A. McKinney, D. M. Lilley, T. Ha), J. Mol. Biol., volume 341, 2004. [bibtex] [pdf]
[17] Single-molecule three-color FRET (S. Hohng, C. Joo, T. Ha), Biophys. J., volume 87, 2004. [bibtex] [pdf]
[16] Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy (M. C. Murphy, I. Rasnik, W. Cheng, T. M. Lohman, T. Ha), Biophys. J., volume 86, 2004. [bibtex] [pdf]
[15] Structural dynamics and processing of nucleic acids revealed by single-molecule spectroscopy (T. Ha), Biochemistry, volume 43, 2004. [bibtex] [pdf]
[14] Single-molecule high-resolution imaging with photobleaching (M. P. Gordon, T. Ha, P. R. Selvin), Proc. Natl. Acad. Sci. U.S.A., volume 101, 2004. [bibtex] [pdf]
[13] Functional analysis of multiple single-stranded DNA-binding proteins from Methanosarcina acetivorans and their effects on DNA synthesis by DNA polymerase BI (J. B. Robbins, M. C. Murphy, B. A. White, R. I. Mackie, T. Ha, I. K. Cann), J. Biol. Chem., volume 279, 2004. [bibtex] [pdf]
[12] Near-complete suppression of quantum dot blinking in ambient conditions (S. Hohng, T. Ha), J. Am. Chem. Soc., volume 126, 2004. [bibtex] [pdf]
[11] 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 (I. Rasnik, S. Myong, W. Cheng, T. M. Lohman, T. Ha), J. Mol. Biol., volume 336, 2004. [bibtex] [pdf]
[10] Discrete and heterogeneous rotational dynamics of single membrane probe dyes in gel phase supported lipid bilayer (B. C. Stevens, T. Ha), J Chem Phys, volume 120, 2004. [bibtex] [pdf]
[9] Conformational flexibility of four-way junctions in RNA (S. Hohng, T. J. Wilson, E. Tan, R. M. Clegg, D. M. Lilley, T. Ha), J. Mol. Biol., volume 336, 2004. [bibtex] [pdf]
[8] Conformational model of the Holliday junction transition deduced from molecular dynamics simulations (J. Yu, T. Ha, K. Schulten), Nucleic Acids Res., volume 32, 2004. [bibtex] [pdf]
2003
[7] A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate (E. Tan, T. J. Wilson, M. K. Nahas, R. M. Clegg, D. M. Lilley, T. Ha), Proc. Natl. Acad. Sci. U.S.A., volume 100, 2003. [bibtex] [pdf]
[6] Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization (A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, P. R. Selvin), Science, volume 300, 2003. [bibtex] [pdf]
[5] Photodestruction intermediates probed by an adjacent reporter molecule (T. Ha, J. Xu), Phys. Rev. Lett., volume 90, 2003. [bibtex] [pdf]
[4] Structural dynamics of individual Holliday junctions (S. A. McKinney, A. C. Declais, D. M. Lilley, T. Ha), Nat. Struct. Biol., volume 10, 2003. [bibtex] [pdf]
2002
[3] Early steps of supported bilayer formation probed by single vesicle fluorescence assays (J. M. Johnson, T. Ha, S. Chu, S. G. Boxer), Biophys. J., volume 83, 2002. [bibtex] [pdf]
[2] Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase (T. Ha, I. Rasnik, W. Cheng, H. P. Babcock, G. H. Gauss, T. M. Lohman, S. Chu), Nature, volume 419, 2002. [bibtex] [pdf]
[1] Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules (H. D. Kim, G. U. Nienhaus, T. Ha, J. W. Orr, J. R. Williamson, S. Chu), Proc. Natl. Acad. Sci. U.S.A., volume 99, 2002. [bibtex] [pdf]