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Complete Publication List

2019
[257] Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS. (M. Bobrovskyy, M. S. Azam, J. K. Frandsen, J. Zhang, A. Poddar, X. Ma, T. M. Henkin, T. Ha, C. K. Vanderpool), In Mol. Microbiol., Mol. Microbiol., 2019. [bibtex] [pdf]
[256] Fight against background noise in stimulated emission depletion nanoscopy. (Y. Ma, T. Ha), In Phys Biol, Phys Biol, 2019. [bibtex] [pdf]
[255] Nuclear speckle fusion via long-range directional motion regulates speckle morphology after transcriptional inhibition. (J. Kim, K. Y. Han, N. Khanna, T. Ha, A. S. Belmont), In J. Cell. Sci., J. Cell. Sci., 2019. [bibtex] [pdf]
[254] Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy. (J. Mitra, M. A. Makurath, T. T. M. Ngo, A. Troitskaia, Y. R. Chemla, T. Ha), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2019. [bibtex] [pdf]
[253] Functional instability allows access to DNA in longer transcription Activator-Like effector (TALE) arrays. (K. Geiger-Schuller, J. Mitra, T. Ha, D. Barrick), In Elife, Elife, 2019. [bibtex] [pdf]
[252] Hexameric helicase G40P unwinds DNA in single base pair steps. (M. Schlierf, G. Wang, X. S. Chen, T. Ha), In Elife, Elife, 2019. [bibtex] [pdf]
[251] Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins. (K. Dubiel, A. R. Myers, A. G. Kozlov, O. Yang, J. Zhang, T. Ha, T. M. Lohman, J. L. Keck), In J. Mol. Biol., J. Mol. Biol., 2019. [bibtex] [pdf]
[250] Contractility kits promote assembly of the mechanoresponsive cytoskeletal network. (P. Kothari, V. Srivastava, V. Aggarwal, I. Tchernyshyov, J. E. Van Eyk, T. Ha, D. N. Robinson), In J. Cell. Sci., J. Cell. Sci., 2019. [bibtex] [pdf]
[249] Junction resolving enzymes use multivalency to keep the Holliday junction dynamic. (R. Zhou, O. Yang, A. C. Déclais, H. Jin, G. H. Gwon, A. D. J. Freeman, Y. Cho, D. M. J. Lilley, T. Ha), In Nat. Chem. Biol., Nat. Chem. Biol., 2019. [bibtex] [pdf]
2018
[248] Publisher Correction: Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. (B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. R. Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, 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. Hübner, 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. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, T. Hugel), In Nat. Methods, Nat. Methods, 2018. [bibtex] [pdf]
[247] 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), In Nat. Struct. Mol. Biol., Nat. Struct. Mol. Biol., 2018. [bibtex] [pdf]
[246] 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), In Sci Rep, Sci Rep, 2018. [bibtex] [pdf]
[245] Understanding the Molecular Mechanisms of the CRISPR Toolbox Using Single Molecule Approaches. (D. Singh, T. Ha), In ACS Chem. Biol., ACS Chem. Biol., 2018. [bibtex] [pdf]
[244] Editorial Overview: Single-Molecule Approaches up to Difficult Challenges in Folding and Dynamics. (Y. Zhang, T. Ha, S. Marqusee), In J. Mol. Biol., J. Mol. Biol., 2018. [bibtex] [pdf]
[243] Mechanism of polypurine tract primer generation by HIV-1 reverse transcriptase. (M. Figiel, M. Krepl, S. Park, J. Poznański, K. Skowronek, A. Gołąb, T. Ha, J. Šponer, M. Nowotny), In J. Biol. Chem., J. Biol. Chem., 2018. [bibtex] [pdf]
[242] Toward Single-Cell Single-Molecule Pull-Down. (X. Wang, S. Park, L. Zeng, A. Jain, T. Ha), In Biophys. J., Biophys. J., 2018. [bibtex] [pdf]
[241] 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), In Mol. Cell, Mol. Cell, 2018. [bibtex] [pdf]
[240] 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2018. [bibtex] [pdf]
[239] Cdc42-dependent modulation of rigidity sensing and cell spreading in tumor repopulating cells. (F. Chowdhury, S. Doğanay, B. J. Leslie, R. Singh, K. Amar, B. Talluri, S. Park, N. Wang, T. Ha), In Biochem. Biophys. Res. Commun., Biochem. Biophys. Res. Commun., 2018. [bibtex] [pdf]
[238] 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), In Biochemistry, Biochemistry, 2018. [bibtex] [pdf]
[237] Mimicking Co-Transcriptional RNA Folding Using a Superhelicase. (B. Hua, S. Panja, Y. Wang, S. A. Woodson, T. Ha), In J. Am. Chem. Soc., J. Am. Chem. Soc., 2018. [bibtex] [pdf]
[236] Single-Molecule FRET Analysis of Replicative Helicases. (S. J. Lee, S. Syed, T. Ha), In Methods Mol. Biol., Methods Mol. Biol., 2018. [bibtex] [pdf]
[235] Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. (B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, 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. Götz, 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. Hübner, 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. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, T. Hugel), In Nat. Methods, Nat. Methods, 2018. [bibtex] [pdf]
[234] Single-Molecule Studies of ssDNA-Binding Proteins Exchange. (O. Yang, T. Ha), In Meth. Enzymol., Meth. Enzymol., 2018. [bibtex] [pdf]
2017
[233] 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), In J. Cell. Sci., J. Cell. Sci., 2017. [bibtex] [pdf]
[232] Single-cell analysis of early antiviral gene expression reveals a determinant of stochastic IFNB1 expression. (S. Doğanay, M. Y. Lee, A. Baum, J. Peh, S. Y. Hwang, J. Y. Yoo, P. J. Hergenrother, A. García-Sastre, S. Myong, T. Ha), In Integr Biol (Camb), Integr Biol (Camb), 2017. [bibtex] [pdf]
[231] 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), In Mol. Biol. Cell, Mol. Biol. Cell, 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), In Nat. Chem. Biol., Nat. Chem. Biol., 2017. [bibtex] [pdf]
[229] 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), In Protein Sci., Protein Sci., 2017. [bibtex] [pdf]
[228] Probing Single Helicase Dynamics on Long Nucleic Acids Through Fluorescence-Force Measurement. (C. T. Lin, T. Ha), In Methods Mol. Biol., Methods Mol. Biol., 2017. [bibtex] [pdf]
[227] Flipping nanoscopy on its head. (J. Xiao, T. Ha), In Science, Science, 2017. [bibtex] [pdf]
[226] Structural biology: Growth factor rattled out of its cage. (T. Ha), In Nature, Nature, 2017. [bibtex] [pdf]
[225] Mapping cell surface adhesion by rotation tracking and adhesion footprinting. (I. T. Li, T. Ha, Y. R. Chemla), In Sci Rep, Sci Rep, 2017. [bibtex] [pdf]
[224] 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), In Nucleic Acids Res., Nucleic Acids Res., 2017. [bibtex] [pdf]
[223] 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), In Science, Science, 2017. [bibtex] [pdf]
[222] Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes. (S. C. Abeysirigunawardena, H. Kim, J. Lai, K. Ragunathan, M. C. Rappé, Z. Luthey-Schulten, T. Ha, S. A. Woodson), In Nat Commun, Nat Commun, 2017. [bibtex] [pdf]
[221] 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. Deschênes), In Nat Commun, Nat Commun, 2017. [bibtex] [pdf]
2016
[220] 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), In Chem. Commun. (Camb.), Chem. Commun. (Camb.), 2016. [bibtex] [pdf]
[219] Single-Molecule Analysis of Lipid-Protein Interactions in Crude Cell Lysates. (E. Arauz, V. Aggarwal, A. Jain, T. Ha, J. Chen), In Anal. Chem., Anal. Chem., 2016. [bibtex] [pdf]
[218] 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), In Nucleic Acids Res., Nucleic Acids Res., 2016. [bibtex] [pdf]
[217] 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), In J. Am. Chem. Soc., J. Am. Chem. Soc., 2016. [bibtex] [pdf]
[216] Probing Nature's Nanomachines One Molecule at a Time. (T. Ha), In Biophys. J., Biophys. J., 2016. [bibtex] [pdf]
[215] Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation. (J. Yoo, H. Kim, A. Aksimentiev, T. Ha), In Nat Commun, Nat Commun, 2016. [bibtex] [pdf]
[214] 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), In ACS Infect Dis, ACS Infect Dis, 2016. [bibtex] [pdf]
[213] 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), In Nano Lett., Nano Lett., 2016. [bibtex] [pdf]
[212] 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), In Nat Commun, Nat Commun, 2016. [bibtex] [pdf]
[211] The light side of the force. (A. Basu, T. Ha), In Elife, Elife, 2016. [bibtex] [pdf]
[210] 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), In Sci Rep, Sci Rep, 2016. [bibtex] [pdf]
[209] Structural dynamics of potassium-channel gating revealed by single-molecule FRET. (S. Wang, R. Vafabakhsh, W. F. Borschel, T. Ha, C. G. Nichols), In Nat. Struct. Mol. Biol., Nat. Struct. Mol. Biol., 2016. [bibtex] [pdf]
[208] Correction: Nanoscale mechanics guides cellular decision making. (Z. Rahil, S. Pedron, X. Wang, T. Ha, B. Harley, D. Leckband), In Integr Biol (Camb), Integr Biol (Camb), 2016. [bibtex] [pdf]
[207] 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. Deflubé, S. Doğanay, L. Banadyga, J. Olejnik, A. J. Hume, E. Ryabchikova, H. Ebihara, N. Kedersha, T. Ha, E. Mühlberger), In J. Virol., J. Virol., 2016. [bibtex] [pdf]
[206] Single-molecule fluorescence microscopy of native macromolecular complexes. (V. Aggarwal, T. Ha), In Curr. Opin. Struct. Biol., Curr. Opin. Struct. Biol., 2016. [bibtex] [pdf]
[205] 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), In J. Virol., J. Virol., 2016. [bibtex] [pdf]
[204] 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), In Nat Commun, Nat Commun, 2016. [bibtex] [pdf]
[203] Nanoscale mechanics guides cellular decision making. (Z. Rahil, S. Pedron, X. Wang, T. Ha, B. Harley, D. Leckband), In Integr Biol (Camb), Integr Biol (Camb), 2016. [bibtex] [pdf]
[202] 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), In Plant Cell, Plant Cell, 2016. [bibtex] [pdf]
[201] 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), In Nano Lett., Nano Lett., 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 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), In Biophys. J., Biophys. J., 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), In Sci Rep, Sci Rep, 2015. [bibtex] [pdf]
[197] Single molecular force across single integrins dictates cell spreading. (F. Chowdhury, I. T. S. Li, B. J. Leslie, S. Doğanay, R. Singh, X. Wang, J. Seong, S. H. Lee, S. Park, N. Wang, T. Ha), In Integr Biol (Camb), Integr Biol (Camb), 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), In J. Biol. Chem., J. Biol. Chem., 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2015. [bibtex] [pdf]
[194] Dual-color three-dimensional STED microscopy with a single high-repetition-rate laser. (K. Y. Han, T. Ha), In Opt Lett, Opt Lett, 2015. [bibtex] [pdf]
[193] A parameter estimation method for fluorescence lifetime data. (D. Sewell, H. Kim, T. Ha, P. Ma), In BMC Res Notes, BMC Res Notes, 2015. [bibtex] [pdf]
[192] Nucleosomes undergo slow spontaneous gaping. (T. T. Ngo, T. Ha), In Nucleic Acids Res., Nucleic Acids Res., 2015. [bibtex] [pdf]
[191] 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), In Elife, Elife, 2015. [bibtex] [pdf]
[190] Protein structure. Engineering of a superhelicase through conformational control. (S. Arslan, R. Khafizov, C. D. Thomas, Y. R. Chemla, T. Ha), In Science, Science, 2015. [bibtex] [pdf]
[189] 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), In Science, Science, 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), In Science, Science, 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), In Cell, Cell, 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), In Elife, Elife, 2015. [bibtex] [pdf]
[185] RNA fluorescence in situ hybridization in cultured mammalian cells. (V. Tripathi, J. Fei, T. Ha, K. V. Prasanth), In Methods Mol. Biol., Methods Mol. Biol., 2015. [bibtex] [pdf]
[184] Dynamic growth and shrinkage govern the pH dependence of RecA filament stability. (S. H. Kim, J. Park, C. Joo, D. Kim, T. Ha), In PLoS ONE, PLoS ONE, 2015. [bibtex] [pdf]
2014
[183] Stoichiometry and assembly of mTOR complexes revealed by single-molecule pulldown. (A. Jain, E. Arauz, V. Aggarwal, N. Ikon, J. Chen, T. Ha), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 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), In J. Am. Chem. Soc., J. Am. Chem. Soc., 2014. [bibtex] [pdf]
[181] 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), In Nat. Methods, Nat. Methods, 2014. [bibtex] [pdf]
[180] 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), In Bioessays, Bioessays, 2014. [bibtex] [pdf]
[179] 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), In Virology, Virology, 2014. [bibtex] [pdf]
[178] Targeting DNA G-quadruplexes with helical small molecules. (S. Müller, K. Laxmi-Reddy, P. V. Jena, B. Baptiste, Z. Dong, F. Godde, T. Ha, R. Rodriguez, S. Balasubramanian, I. Huc), In Chembiochem, Chembiochem, 2014. [bibtex] [pdf]
[177] Cooperative conformational transitions keep RecA filament active during ATPase cycle. (S. H. Kim, K. Ragunathan, J. Park, C. Joo, D. Kim, T. Ha), In J. Am. Chem. Soc., J. Am. Chem. Soc., 2014. [bibtex] [pdf]
[176] 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2014. [bibtex] [pdf]
[175] Single-molecule methods leap ahead. (T. Ha), In Nat. Methods, Nat. Methods, 2014. [bibtex] [pdf]
[174] 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. Doğanay, Y. Li, H. Jia, T. Ha, Y. Wang, B. Huang, N. Wang), In Nat Commun, Nat Commun, 2014. [bibtex] [pdf]
[173] 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), In J Chem Theory Comput, J Chem Theory Comput, 2014. [bibtex] [pdf]
[172] Biophysics. Ultraslow relaxation of confined DNA. (Y. R. Chemla, T. Ha), In Science, Science, 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), In J. Mol. Biol., J. Mol. Biol., 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), In Elife, Elife, 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), In Nucleic Acids Res., Nucleic Acids Res., 2014. [bibtex] [pdf]
[168] Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase. (S. Syed, M. Pandey, S. S. Patel, T. Ha), In Cell Rep, Cell Rep, 2014. [bibtex] [pdf]
[167] 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2014. [bibtex] [pdf]
[166] 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), In Cell Host Microbe, Cell Host Microbe, 2014. [bibtex] [pdf]
[165] 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), In Nature, Nature, 2014. [bibtex] [pdf]
[164] Single-molecule optical spectroscopy. (M. Orrit, T. Ha, V. Sandoghdar), In Chem Soc Rev, Chem Soc Rev, 2014. [bibtex] [pdf]
[163] 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. Doğanay, B. Chung, Z. Toth, K. Brulois, S. Lee, Z. Kanketayeva, P. Feng, T. Ha, J. U. Jung), In J. Virol., J. Virol., 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 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), In Archaea, Archaea, 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), In PLoS ONE, PLoS ONE, 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), In J. Am. Chem. Soc., J. Am. Chem. Soc., 2013. [bibtex] [pdf]
[158] Watching DNA breath one molecule at a time. (J. Fei, T. Ha), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2013. [bibtex] [pdf]
[157] 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. García-Sastre), In EMBO Rep., EMBO Rep., 2013. [bibtex] [pdf]
[156] Molecular mechanism of sequence-dependent stability of RecA filament. (S. H. Kim, C. Joo, T. Ha, D. Kim), In Nucleic Acids Res., Nucleic Acids Res., 2013. [bibtex] [pdf]
[155] Single-molecule approaches embrace molecular cohorts. (T. Ha), In Cell, Cell, 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), In Nat Chem, Nat Chem, 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), In J. Mol. Biol., J. Mol. Biol., 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), In J. Biol. Chem., J. Biol. Chem., 2013. [bibtex] [pdf]
[151] Defining single molecular forces required to activate integrin and notch signaling. (X. Wang, T. Ha), In Science, Science, 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), In RNA, RNA, 2013. [bibtex] [pdf]
[149] Single-molecule nanometry for biological physics. (H. Kim, T. Ha), In Rep Prog Phys, Rep Prog Phys, 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2013. [bibtex] [pdf]
[147] 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), In EMBO J., EMBO J., 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), In Nat Commun, Nat Commun, 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), In PLoS Genet., PLoS Genet., 2013. [bibtex] [pdf]
2012
[144] Prism-type total internal reflection microscopy for single-molecule FRET. (C. Joo, T. Ha), In Cold Spring Harb Protoc, Cold Spring Harb Protoc, 2012. [bibtex] [pdf]
[143] RecA filament sliding on DNA facilitates homology search. (K. Ragunathan, C. Liu, T. Ha), In Elife, Elife, 2012. [bibtex] [pdf]
[142] Single-molecule FRET with total internal reflection microscopy. (C. Joo, T. Ha), In Cold Spring Harb Protoc, Cold Spring Harb Protoc, 2012. [bibtex] [pdf]
[141] Activated GTPase movement on an RNA scaffold drives co-translational protein targeting. (K. Shen, S. Arslan, D. Akopian, T. Ha, S. O. Shan), In Nature, Nature, 2012. [bibtex] [pdf]
[140] Objective-type total internal reflection microscopy (emission) for single-molecule FRET. (C. Joo, T. Ha), In Cold Spring Harb Protoc, Cold Spring Harb Protoc, 2012. [bibtex] [pdf]
[139] Objective-type total internal reflection microscopy (excitation) for single-molecule FRET. (C. Joo, T. Ha), In Cold Spring Harb Protoc, Cold Spring Harb Protoc, 2012. [bibtex] [pdf]
[138] Imaging and identifying impurities in single-molecule FRET studies. (C. Joo, T. Ha), In Cold Spring Harb Protoc, Cold Spring Harb Protoc, 2012. [bibtex] [pdf]
[137] A helicase with an extra spring in its step. (M. Schlierf, T. Ha), In Cell, Cell, 2012. [bibtex] [pdf]
[136] Preparing sample chambers for single-molecule FRET. (C. Joo, T. Ha), In Cold Spring Harb Protoc, Cold Spring Harb Protoc, 2012. [bibtex] [pdf]
[135] Labeling proteins for single-molecule FRET. (C. Joo, T. Ha), In Cold Spring Harb Protoc, Cold Spring Harb Protoc, 2012. [bibtex] [pdf]
[134] Labeling DNA (or RNA) for single-molecule FRET. (C. Joo, T. Ha), In Cold Spring Harb Protoc, Cold Spring Harb Protoc, 2012. [bibtex] [pdf]
[133] 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), In J. Biol. Chem., J. Biol. Chem., 2012. [bibtex] [pdf]
[132] 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), In Mol. Cell. Biol., Mol. Cell. Biol., 2012. [bibtex] [pdf]
[131] Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. (R. Vafabakhsh, T. Ha), In Science, Science, 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. Doğanay, R. Vafabakhsh, T. Ha, P. Palese), In J. Virol., J. Virol., 2012. [bibtex] [pdf]
[129] Elastic coupling between RNA degradation and unwinding by an exoribonuclease. (G. Lee, M. A. Bratkowski, F. Ding, A. Ke, T. Ha), In Science, Science, 2012. [bibtex] [pdf]
[128] 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), In J Phys Chem B, J Phys Chem B, 2012. [bibtex] [pdf]
[127] Single-molecule imaging: a collagenase pauses before embarking on a killing spree. (G. Lee, T. Ha), In Curr. Biol., Curr. Biol., 2012. [bibtex] [pdf]
[126] One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis. (Y. Y. Chou, R. Vafabakhsh, S. Doğanay, Q. Gao, T. Ha, P. Palese), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2012. [bibtex] [pdf]
[125] A rule of seven in Watson-Crick base-pairing of mismatched sequences. (I. I. Cisse, H. Kim, T. Ha), In Nat. Struct. Mol. Biol., Nat. Struct. Mol. Biol., 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), In Nat Protoc, Nat Protoc, 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), In Nat. Methods, Nat. Methods, 2012. [bibtex] [pdf]
[122] Single-molecule pull-down for studying protein interactions. (A. Jain, R. Liu, Y. K. Xiang, T. Ha), In Nat Protoc, Nat Protoc, 2012. [bibtex] [pdf]
[121] Opening-closing dynamics of the mitochondrial transcription pre-initiation complex. (H. Kim, G. Q. Tang, S. S. Patel, T. Ha), In Nucleic Acids Res., Nucleic Acids Res., 2012. [bibtex] [pdf]
[120] Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging. (T. Ha, P. Tinnefeld), In Annu Rev Phys Chem, Annu Rev Phys Chem, 2012. [bibtex] [pdf]
[119] Single-molecule analysis of SSB dynamics on single-stranded DNA. (R. Zhou, T. Ha), In Methods Mol. Biol., Methods Mol. Biol., 2012. [bibtex] [pdf]
[118] Single-molecule views of protein movement on single-stranded DNA. (T. Ha, A. G. Kozlov, T. M. Lohman), In Annu Rev Biophys, Annu Rev Biophys, 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), In Nano Lett., Nano Lett., 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), In Nature, Nature, 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2011. [bibtex] [pdf]
[114] A single-molecule view of chaperonin cooperativity. (T. Ha, S. Myong), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2011. [bibtex] [pdf]
[113] Single-molecule nanopositioning: structural transitions of a helicase-DNA complex during ATP hydrolysis. (H. Balci, S. Arslan, S. Myong, T. M. Lohman, T. Ha), In Biophys. J., Biophys. J., 2011. [bibtex] [pdf]
[112] 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), In J. Mol. Biol., J. Mol. Biol., 2011. [bibtex] [pdf]
[111] Real-time observation of strand exchange reaction with high spatiotemporal resolution. (K. Ragunathan, C. Joo, T. Ha), In Structure, Structure, 2011. [bibtex] [pdf]
[110] 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), In J. Am. Chem. Soc., J. Am. Chem. Soc., 2011. [bibtex] [pdf]
[109] 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), In Cell, Cell, 2011. [bibtex] [pdf]
[108] Tyrosine phosphorylation enhances RAD52-mediated annealing by modulating its DNA binding. (M. Honda, Y. Okuno, J. Yoo, T. Ha, M. Spies), In EMBO J., EMBO J., 2011. [bibtex] [pdf]
[107] 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2011. [bibtex] [pdf]
[106] Editorial on nanobiology. (S. K. Kim, T. Ha, J. P. Schermann), In Phys Chem Chem Phys, Phys Chem Chem Phys, 2011. [bibtex] [pdf]
[105] Single-molecule analysis reveals three phases of DNA degradation by an exonuclease. (G. Lee, J. Yoo, B. J. Leslie, T. Ha), In Nat. Chem. Biol., Nat. Chem. Biol., 2011. [bibtex] [pdf]
[104] 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), In Nature, Nature, 2011. [bibtex] [pdf]
[103] Forcing a connection: impacts of single-molecule force spectroscopy on in vivo tension sensing. (M. D. Brenner, R. Zhou, T. Ha), In Biopolymers, Biopolymers, 2011. [bibtex] [pdf]
[102] Ultrahigh-resolution optical trap with single-fluorophore sensitivity. (M. J. Comstock, T. Ha, Y. R. Chemla), In Nat. Methods, Nat. Methods, 2011. [bibtex] [pdf]
[101] 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), In Biophys. J., Biophys. J., 2011. [bibtex] [pdf]
[100] Seeing a molecular machine self-renew. (X. Shi, T. Ha), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 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), In PLoS Biol., PLoS Biol., 2011. [bibtex] [pdf]
[98] Homochirality and the origin of life. Editorial of the PCCP themed issue. (S. K. Kim, T. Ha, J. P. Schermann), In Phys Chem Chem Phys, Phys Chem Chem Phys, 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), In Anal. Chem., Anal. Chem., 2010. [bibtex] [pdf]
[96] Reversible and controllable nanolocomotion of an RNA-processing machinery. (G. Lee, S. Hartung, K. P. Hopfner, T. Ha), In Nano Lett., Nano Lett., 2010. [bibtex] [pdf]
[95] Single-molecule four-color FRET. (J. Lee, S. Lee, K. Ragunathan, C. Joo, T. Ha, S. Hohng), In Angew. Chem. Int. Ed. Engl., Angew. Chem. Int. Ed. Engl., 2010. [bibtex] [pdf]
[94] Advances in mass spectrometry for biological science. (S. K. Kim, T. Ha, J. P. Schermann), In Phys Chem Chem Phys, Phys Chem Chem Phys, 2010. [bibtex] [pdf]
[93] 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), In EMBO J., EMBO J., 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), In J. Mol. Biol., J. Mol. Biol., 2010. [bibtex] [pdf]
[91] Water in biological systems. (S. K. Kim, T. Ha, J. P. Schermann), In Phys Chem Chem Phys, Phys Chem Chem Phys, 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), In Nat Commun, Nat Commun, 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), In Cell, Cell, 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), In Anal. Chem., Anal. Chem., 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), In Nature, Nature, 2010. [bibtex] [pdf]
[86] Inching over hurdles: how DNA helicases move on crowded lattices. (M. Spies, T. Ha), In Cell Cycle, Cell Cycle, 2010. [bibtex] [pdf]
[85] Insight into helicase mechanism and function revealed through single-molecule approaches. (J. G. Yodh, M. Schlierf, T. Ha), In Q. Rev. Biophys., Q. Rev. Biophys., 2010. [bibtex] [pdf]
[84] 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), In Nucleic Acids Res., Nucleic Acids Res., 2010. [bibtex] [pdf]
[83] Biomolecular structures: from isolated molecules to the cell crowded medium. (S. K. Kim, T. Ha, J. P. Schermann), In Phys Chem Chem Phys, Phys Chem Chem Phys, 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), In J Phys Chem B, J Phys Chem B, 2010. [bibtex] [pdf]
[81] 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), In ACS Chem Neurosci, ACS Chem Neurosci, 2010. [bibtex] [pdf]
[80] 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), In Biochemistry, Biochemistry, 2010. [bibtex] [pdf]
[79] Stepwise translocation of nucleic acid motors. (S. Myong, T. Ha), In Curr. Opin. Struct. Biol., Curr. Opin. Struct. Biol., 2010. [bibtex] [pdf]
[78] Force-fluorescence spectroscopy at the single-molecule level. (R. Zhou, M. Schlierf, T. Ha), In Meth. Enzymol., Meth. Enzymol., 2010. [bibtex] [pdf]
[77] Real-time observation of G-quadruplex dynamics using single-molecule FRET microscopy. (B. Okumus, T. Ha), In Methods Mol. Biol., Methods Mol. Biol., 2010. [bibtex] [pdf]
[76] Single-molecule FRET analysis of helicase functions. (E. Rothenberg, T. Ha), In Methods Mol. Biol., Methods Mol. Biol., 2010. [bibtex] [pdf]
2009
[75] 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), In Nature, Nature, 2009. [bibtex] [pdf]
[74] 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2009. [bibtex] [pdf]
[73] Single molecule nanocontainers made porous using a bacterial toxin. (B. Okumus, S. Arslan, S. M. Fengler, S. Myong, T. Ha), In J. Am. Chem. Soc., J. Am. Chem. Soc., 2009. [bibtex] [pdf]
[72] SSB protein diffusion on single-stranded DNA stimulates RecA filament formation. (R. Roy, A. G. Kozlov, T. M. Lohman, T. Ha), In Nature, Nature, 2009. [bibtex] [pdf]
[71] 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), In Mol. Cell, Mol. Cell, 2009. [bibtex] [pdf]
[70] 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), In J. Am. Chem. Soc., J. Am. Chem. Soc., 2009. [bibtex] [pdf]
[69] C2AB: a molecular glue for lipid vesicles with a negatively charged surface. (J. Diao, T. Y. Yoon, Z. Su, Y. K. Shin, T. Ha), In Langmuir, Langmuir, 2009. [bibtex] [pdf]
[68] Fluorescent lifetime trajectories of a single fluorophore reveal reaction intermediates during transcription initiation. (M. Sorokina, H. R. Koh, S. S. Patel, T. Ha), In J. Am. Chem. Soc., J. Am. Chem. Soc., 2009. [bibtex] [pdf]
[67] Photonics: How nanocrystals lost their blink. (T. Ha), In Nature, Nature, 2009. [bibtex] [pdf]
[66] DNA nanotechnology: a nanomachine goes live. (Y. Ishitsuka, T. Ha), In Nat Nanotechnol, Nat Nanotechnol, 2009. [bibtex] [pdf]
[65] 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2009. [bibtex] [pdf]
[64] 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), In Science, Science, 2009. [bibtex] [pdf]
[63] 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. Höbartner, T. Ha, S. K. Silverman, M. S. Strano), In Nat Nanotechnol, Nat Nanotechnol, 2009. [bibtex] [pdf]
[62] 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), In EMBO J., EMBO J., 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 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), In J. Bacteriol., J. Bacteriol., 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2008. [bibtex] [pdf]
[57] The SNARE complex from yeast is partially unstructured on the membrane. (Z. Su, Y. Ishitsuka, T. Ha, Y. K. Shin), In Structure, Structure, 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), In Nat. Struct. Mol. Biol., Nat. Struct. Mol. Biol., 2008. [bibtex] [pdf]
[55] Branch migration enzyme as a Brownian ratchet. (I. Rasnik, Y. J. Jeong, S. A. McKinney, V. Rajagopal, S. S. Patel, T. Ha), In EMBO J., EMBO J., 2008. [bibtex] [pdf]
[54] Spontaneous intersubunit rotation in single ribosomes. (P. V. Cornish, D. N. Ermolenko, H. F. Noller, T. Ha), In Mol. Cell, Mol. Cell, 2008. [bibtex] [pdf]
[53] 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), In Mol. Cell, Mol. Cell, 2008. [bibtex] [pdf]
[52] A practical guide to single-molecule FRET. (R. Roy, S. Hohng, T. Ha), In Nat. Methods, Nat. Methods, 2008. [bibtex] [pdf]
[51] Advances in single-molecule fluorescence methods for molecular biology. (C. Joo, H. Balci, Y. Ishitsuka, C. Buranachai, T. Ha), In Annu. Rev. Biochem., Annu. Rev. Biochem., 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), In Nat. Chem. Biol., Nat. Chem. Biol., 2007. [bibtex] [pdf]
[49] How directional translocation is regulated in a DNA helicase motor. (J. Yu, T. Ha, K. Schulten), In Biophys. J., Biophys. J., 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), In J. Biol. Chem., J. Biol. Chem., 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), In Science, Science, 2007. [bibtex] [pdf]
[46] Fueling protein DNA interactions inside porous nanocontainers. (I. Cisse, B. Okumus, C. Joo, T. Ha), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 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), In Science, Science, 2007. [bibtex] [pdf]
[44] 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), In J. Am. Chem. Soc., J. Am. Chem. Soc., 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), In J. Mol. Biol., J. Mol. Biol., 2007. [bibtex] [pdf]
[42] Need for speed: mechanical regulation of a replicative helicase. (T. Ha), In Cell, Cell, 2007. [bibtex] [pdf]
[41] A survey of single-molecule techniques in chemical biology. (P. V. Cornish, T. Ha), In ACS Chem. Biol., ACS Chem. Biol., 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. Régnier, T. Ha), In Nucleic Acids Res., Nucleic Acids Res., 2007. [bibtex] [pdf]
2006
[39] Multiple intermediates in SNARE-induced membrane fusion. (T. Y. Yoon, B. Okumus, F. Zhang, Y. K. Shin, T. Ha), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2006. [bibtex] [pdf]
[38] Nonblinking and long-lasting single-molecule fluorescence imaging. (I. Rasnik, S. A. McKinney, T. Ha), In Nat. Methods, Nat. Methods, 2006. [bibtex] [pdf]
[37] Structure-based model of the stepping motor of PcrA helicase. (J. Yu, T. Ha, K. Schulten), In Biophys. J., Biophys. J., 2006. [bibtex] [pdf]
[36] Analysis of single-molecule FRET trajectories using hidden Markov modeling. (S. A. McKinney, C. Joo, T. Ha), In Biophys. J., Biophys. J., 2006. [bibtex] [pdf]
[35] 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), In J. Bacteriol., J. Bacteriol., 2006. [bibtex] [pdf]
[34] Real-time observation of RecA filament dynamics with single monomer resolution. (C. Joo, S. A. McKinney, M. Nakamura, I. Rasnik, S. Myong, T. Ha), In Cell, Cell, 2006. [bibtex] [pdf]
[33] 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2006. [bibtex] [pdf]
[32] Bridging conformational dynamics and function using single-molecule spectroscopy. (S. Myong, B. C. Stevens, T. Ha), In Structure, Structure, 2006. [bibtex] [pdf]
[31] Single molecule nanometronome. (C. Buranachai, S. A. McKinney, T. Ha), In Nano Lett., Nano Lett., 2006. [bibtex] [pdf]
[30] Unraveling helicase mechanisms one molecule at a time. (I. Rasnik, S. Myong, T. Ha), In Nucleic Acids Res., Nucleic Acids Res., 2006. [bibtex] [pdf]
2005
[29] Extreme conformational diversity in human telomeric DNA. (J. Y. Lee, B. Okumus, D. S. Kim, T. Ha), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2005. [bibtex] [pdf]
[28] Repetitive shuttling of a motor protein on DNA. (S. Myong, I. Rasnik, C. Joo, T. M. Lohman, T. Ha), In Nature, Nature, 2005. [bibtex] [pdf]
[27] 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), In Biophys. J., Biophys. J., 2005. [bibtex] [pdf]
[26] Surfaces and orientations: much to FRET about? (I. Rasnik, S. A. McKinney, T. Ha), In Acc. Chem. Res., Acc. Chem. Res., 2005. [bibtex] [pdf]
[25] Single-molecule quantum-dot fluorescence resonance energy transfer. (S. Hohng, T. Ha), In Chemphyschem, Chemphyschem, 2005. [bibtex] [pdf]
[24] Observing spontaneous branch migration of Holliday junctions one step at a time. (S. A. McKinney, A. D. Freeman, D. M. Lilley, T. Ha), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2005. [bibtex] [pdf]
[23] 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), In J. Biol. Chem., J. Biol. Chem., 2005. [bibtex] [pdf]
[22] Stereospecific effects determine the structure of a four-way DNA junction. (J. Liu, A. C. Déclais, S. A. McKinney, T. Ha, D. G. Norman, D. M. Lilley), In Chem. Biol., Chem. Biol., 2005. [bibtex] [pdf]
2004
[21] 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), In Nat. Struct. Mol. Biol., Nat. Struct. Mol. Biol., 2004. [bibtex] [pdf]
[20] Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic. (B. Okumus, T. J. Wilson, D. M. Lilley, T. Ha), In Biophys. J., Biophys. J., 2004. [bibtex] [pdf]
[19] 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), In J. Mol. Biol., J. Mol. Biol., 2004. [bibtex] [pdf]
[18] Single-molecule three-color FRET. (S. Hohng, C. Joo, T. Ha), In Biophys. J., Biophys. J., 2004. [bibtex] [pdf]
[17] Single-molecule high-resolution imaging with photobleaching. (M. P. Gordon, T. Ha, P. R. Selvin), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2004. [bibtex] [pdf]
[16] Structural dynamics and processing of nucleic acids revealed by single-molecule spectroscopy. (T. Ha), In Biochemistry, Biochemistry, 2004. [bibtex] [pdf]
[15] Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy. (M. C. Murphy, I. Rasnik, W. Cheng, T. M. Lohman, T. Ha), In Biophys. J., Biophys. J., 2004. [bibtex] [pdf]
[14] Conformational flexibility of four-way junctions in RNA. (S. Hohng, T. J. Wilson, E. Tan, R. M. Clegg, D. M. Lilley, T. Ha), In J. Mol. Biol., J. Mol. Biol., 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), In J. Biol. Chem., J. Biol. Chem., 2004. [bibtex] [pdf]
[12] Discrete and heterogeneous rotational dynamics of single membrane probe dyes in gel phase supported lipid bilayer. (B. C. Stevens, T. Ha), In J Chem Phys, J Chem Phys, 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), In J. Mol. Biol., J. Mol. Biol., 2004. [bibtex] [pdf]
[10] Near-complete suppression of quantum dot blinking in ambient conditions. (S. Hohng, T. Ha), In J. Am. Chem. Soc., J. Am. Chem. Soc., 2004. [bibtex] [pdf]
[9] Conformational model of the Holliday junction transition deduced from molecular dynamics simulations. (J. Yu, T. Ha, K. Schulten), In Nucleic Acids Res., Nucleic Acids Res., 2004. [bibtex] [pdf]
2003
[8] 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2003. [bibtex] [pdf]
[7] 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), In Science, Science, 2003. [bibtex] [pdf]
[6] Photodestruction intermediates probed by an adjacent reporter molecule. (T. Ha, J. Xu), In Phys. Rev. Lett., Phys. Rev. Lett., 2003. [bibtex] [pdf]
[5] Structural dynamics of individual Holliday junctions. (S. A. McKinney, A. C. Déclais, D. M. Lilley, T. Ha), In Nat. Struct. Biol., Nat. Struct. Biol., 2003. [bibtex] [pdf]
2002
[4] Early steps of supported bilayer formation probed by single vesicle fluorescence assays. (J. M. Johnson, T. Ha, S. Chu, S. G. Boxer), In Biophys. J., Biophys. J., 2002. [bibtex] [pdf]
[3] 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), In Nature, Nature, 2002. [bibtex] [pdf]
[2] 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), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2002. [bibtex] [pdf]
[1] 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), In Blood Cells Mol. Dis., Blood Cells Mol. Dis., . [bibtex] [pdf]