[281] | DNA mechanics and its biological impact. (Basu, A., Bobrovnikov, D. G. and Ha, T.), In J Mol Biol, 2021. |
[280] | Real-time observation of Cas9 postcatalytic domain motions. (Wang, Y., Mallon, J., Wang, H., Singh, D., Hyun Jo, M., Hua, B., Bailey, S. and Ha, T.), In Proc Natl Acad Sci U S A, 2021. |
[279] | Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA. (Poddar, A., Azam, M. S., Kayikcioglu, T., Bobrovskyy, M., Zhang, J., Ma, X., Labhsetwar, P., Fei, J., Singh, D., Luthey-Schulten, Z., Vanderpool, C. K. and Ha, T.), In Nat Commun, 2021. |
[278] | Measuring DNA mechanics on the genome scale. (Basu, A., Bobrovnikov, D. G., Qureshi, Z., Kayikcioglu, T., Ngo, T. T. M., Ranjan, A., Eustermann, S., Cieza, B., Morgan, M. T., Hejna, M., Rube, H. T., Hopfner, K. P., Wolberger, C., Song, J. S. and Ha, T.), In Nature, 2021. |
[277] | ALS/FTLD-Linked Mutations in FUS Glycine Residues Cause Accelerated Gelation and Reduced Interactions with Wild-Type FUS. (Rhine, K., Makurath, M. A., Liu, J., Skanchy, S., Lopez, C., Catalan, K. F., Ma, Y., Fare, C. M., Shorter, J., Ha, T., Chemla, Y. R. and Myong, S.), In Mol Cell, 2020. |
[276] | Increasing kinase domain proximity promotes MST2 autophosphorylation during Hippo signaling. (Tran, T., Mitra, J., Ha, T. and Kavran, J. M.), In J Biol Chem, 2020. |
[275] | Force-dependent trans-endocytosis by breast cancer cells depletes costimulatory receptor CD80 and attenuates T cell activation. (Park, S., Shi, Y., Kim, B. C., Jo, M. H., Cruz, L. O., Gou, Z., Ha, T., Lu, L. F., Reich, D. H. and Chen, Y.), In Biosens Bioelectron, 2020. |
[274] | COL2A1 Is a Novel Biomarker of Melanoma Tumor Repopulating Cells. (Talluri, B., Amar, K., Saul, M., Shireen, T., Konjufca, V., Ma, J., Ha, T. and Chowdhury, F.), In Biomedicines, 2020. |
[273] | ORCA/LRWD1 Regulates Homologous Recombination at ALT-Telomeres by Modulating Heterochromatin Organization. (), In iScience, 2020. |
[272] | Real-time monitoring of single ZTP riboswitches reveals a complex and kinetically controlled decision landscape. (Hua, B., Jones, C. P., Mitra, J., Murray, P. J., Rosenthal, R., Ferré-D'Amaré, A. R. and Ha, T.), In Nat Commun, 2020. |
[271] | Stochastic Analysis Demonstrates the Dual Role of Hfq in Chaperoning E. coli Sugar Shock Response. (Bianchi, D. M., Brier, T. A., Poddar, A., Azam, M. S., Vanderpool, C. K., Ha, T. and Luthey-Schulten, Z.), In Front Mol Biosci, 2020. |
[270] | ALS/FTLD-Linked Mutations in FUS Glycine Residues Cause Accelerated Gelation and Reduced Interactions with Wild-Type FUS. (Rhine, K., Makurath, M. A., Liu, J., Skanchy, S., Lopez, C., Catalan, K. F., Ma, Y., Fare, C. M., Shorter, J., Ha, T., Chemla, Y. R. and Myong, S.), In Mol Cell, 2020. |
[269] | E. coli Rep helicase and RecA recombinase unwind G4 DNA and are important for resistance to G4-stabilizing ligands. (Paul, T., Voter, A. F., Cueny, R. R., Gavrilov, M., Ha, T., Keck, J. L. and Myong, S.), In Nucleic Acids Res, 2020. |
[268] | Light-controlled twister ribozyme with single-molecule detection resolves RNA function in time and space. (Korman, A., Sun, H., Hua, B., Yang, H., Capilato, J. N., Paul, R., Panja, S., Ha, T., Greenberg, M. M. and Woodson, S. A.), In Proc Natl Acad Sci U S A, 2020. |
[267] | Crystal structure and ligand-induced folding of the SAM/SAH riboswitch. (Huang, L., Liao, T. W., Wang, J., Ha, T. and Lilley, D. M. J.), In Nucleic Acids Res, 2020. |
[266] | Very fast CRISPR on demand. (), In Science, 2020. |
[265] | Just Took a DNA Test, Turns Out 100% Not That Phase. (Gitler, A. D., Shorter, J., Ha, T. and Myong, S.), In Mol Cell, 2020. |
[264] | Single-Molecule Analysis and Engineering of DNA Motors. (Mohapatra, S., Lin, C. T., Feng, X. A., Basu, A. and Ha, T.), In Chem Rev, 2020. |
[263] | Real-Time Measurement of Molecular Tension during Cell Adhesion and Migration Using Multiplexed Differential Analysis of Tension Gauge Tethers. (Jo, M. H., Cottle, W. T. and Ha, T.), In ACS Biomater Sci Eng, 2019. |
[262] | Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS. (Bobrovskyy, M., Azam, M. S., Frandsen, J. K., Zhang, J., Poddar, A., Ma, X., Henkin, T. M., Ha, T. and Vanderpool, C. K.), In Mol Microbiol, 2019. |
[261] | Strategy for Compositional Analysis of the Hair Cell Mechanotransduction Complex Using TIRF Microscopy. (Clark, S., Elferich, J., Gai, J., Goehring, A., Mitra, J., Ha, T. and Gouaux, E.), In Microsc Microanal, 2019. |
[260] | Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases. (), In Nat Commun, 2019. |
[259] | Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding. (Okafor, I. C., Singh, D., Wang, Y., Jung, M., Wang, H., Mallon, J., Bailey, S., Lee, J. K. and Ha, T.), In Nucleic Acids Res, 2019. |
[258] | Nanomechanics and co-transcriptional folding of Spinach and Mango. (), In Nat Commun, 2019. |
[257] | Streamlining effects of extra telomeric repeat on telomeric DNA folding revealed by fluorescence-force spectroscopy. (Mitra, J. and Ha, T.), In Nucleic Acids Res, 2019. |
[256] | Hexameric helicase G40P unwinds DNA in single base pair steps. (), In Elife, 2019. |
[255] | Functional instability allows access to DNA in longer transcription Activator-Like effector (TALE) arrays. (), In Elife, 2019. |
[254] | Nuclear speckle fusion via long-range directional motion regulates speckle morphology after transcriptional inhibition. (Kim, J., Han, K. Y., Khanna, N., Ha, T. and Belmont, A. S.), In J Cell Sci, 2019. |
[253] | Contractility kits promote assembly of the mechanoresponsive cytoskeletal network. (Kothari, P., Srivastava, V., Aggarwal, V., Tchernyshyov, I., Van Eyk, J. E., Ha, T. and Robinson, D. N.), In J Cell Sci, 2019. |
[252] | Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy. (Mitra, J., Makurath, M. A., Ngo, T. T. M., Troitskaia, A., Chemla, Y. R. and Ha, T.), In Proc Natl Acad Sci U S A, 2019. |
[251] | Junction resolving enzymes use multivalency to keep the Holliday junction dynamic. (Zhou, R., Yang, O., Déclais, A. C., Jin, H., Gwon, G. H., Freeman, A. D. J., Cho, Y., Lilley, D. M. J. and Ha, T.), In Nat Chem Biol, 2019. |
[250] | Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins. (Dubiel, K., Myers, A. R., Kozlov, A. G., Yang, O., Zhang, J., Ha, T., Lohman, T. M. and Keck, J. L.), In J Mol Biol, 2019. |
[249] | Fight against background noise in stimulated emission depletion nanoscopy. (), In Phys Biol, 2019. |
[248] | Publisher Correction: Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. (Hellenkamp, B., Schmid, S., Doroshenko, O., Opanasyuk, O., Kühnemuth, R., Adariani, S. R., Ambrose, B., Aznauryan, M., Barth, A., Birkedal, V., Bowen, M. E., Chen, H., Cordes, T., Eilert, T., Fijen, C., Gebhardt, C., Götz, M., Gouridis, G., Gratton, E., Ha, T., Hao, P., Hanke, C. A., Hartmann, A., Hendrix, J., Hildebrandt, L. L., Hirschfeld, V., Hohlbein, J., Hua, B., Hübner, C. G., Kallis, E., Kapanidis, A. N., Kim, J. Y., Krainer, G., Lamb, D. C., Lee, N. K., Lemke, E. A., Levesque, B., Levitus, M., McCann, J. J., Naredi-Rainer, N., Nettels, D., Ngo, T., Qiu, R., Robb, N. C., Röcker, C., Sanabria, H., Schlierf, M., Schröder, T., Schuler, B., Seidel, H., Streit, L., Thurn, J., Tinnefeld, P., Tyagi, S., Vandenberk, N., Vera, A. M., Weninger, K. R., Wünsch, B., Yanez-Orozco, I. S., Michaelis, J., Seidel, C. A. M., Craggs, T. D. and Hugel, T.), In Nat Methods, 2018. |
[247] | Cdc42-dependent modulation of rigidity sensing and cell spreading in tumor repopulating cells. (Chowdhury, F., Doğanay, S., Leslie, B. J., Singh, R., Amar, K., Talluri, B., Park, S., Wang, N. and Ha, T.), In Biochem Biophys Res Commun, 2018. |
[246] | Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. (Hellenkamp, B., Schmid, S., Doroshenko, O., Opanasyuk, O., Kühnemuth, R., Rezaei Adariani, S., Ambrose, B., Aznauryan, M., Barth, A., Birkedal, V., Bowen, M. E., Chen, H., Cordes, T., Eilert, T., Fijen, C., Gebhardt, C., Götz, M., Gouridis, G., Gratton, E., Ha, T., Hao, P., Hanke, C. A., Hartmann, A., Hendrix, J., Hildebrandt, L. L., Hirschfeld, V., Hohlbein, J., Hua, B., Hübner, C. G., Kallis, E., Kapanidis, A. N., Kim, J. Y., Krainer, G., Lamb, D. C., Lee, N. K., Lemke, E. A., Levesque, B., Levitus, M., McCann, J. J., Naredi-Rainer, N., Nettels, D., Ngo, T., Qiu, R., Robb, N. C., Röcker, C., Sanabria, H., Schlierf, M., Schröder, T., Schuler, B., Seidel, H., Streit, L., Thurn, J., Tinnefeld, P., Tyagi, S., Vandenberk, N., Vera, A. M., Weninger, K. R., Wünsch, B., Yanez-Orozco, I. S., Michaelis, J., Seidel, C. A. M., Craggs, T. D. and Hugel, T.), In Nat Methods, 2018. |
[245] | Single-Molecule FRET Analysis of Replicative Helicases. (Lee, S. J., Syed, S. and Ha, T.), In Methods Mol Biol, 2018. |
[244] | Mimicking Co-Transcriptional RNA Folding Using a Superhelicase. (Hua, B., Panja, S., Wang, Y., Woodson, S. A. and Ha, T.), In J Am Chem Soc, 2018. |
[243] | Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis. (Singh, D., Wang, Y., Mallon, J., Yang, O., Fei, J., Poddar, A., Ceylan, D., Bailey, S. and Ha, T.), In Nat Struct Mol Biol, 2018. |
[242] | Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a). (Singh, D., Mallon, J., Poddar, A., Wang, Y., Tippana, R., Yang, O., Bailey, S. and Ha, T.), In Proc Natl Acad Sci U S A, 2018. |
[241] | The Single-Molecule Centroid Localization Algorithm Improves the Accuracy of Fluorescence Binding Assays. (), In Biochemistry, 2018. |
[240] | Toward Single-Cell Single-Molecule Pull-Down. (Wang, X., Park, S., Zeng, L., Jain, A. and Ha, T.), In Biophys J, 2018. |
[239] | Editorial Overview: Single-Molecule Approaches up to Difficult Challenges in Folding and Dynamics. (Zhang, Y., Ha, T. and Marqusee, S.), In J Mol Biol, 2018. |
[238] | Understanding the Molecular Mechanisms of the CRISPR Toolbox Using Single Molecule Approaches. (Singh, D. and Ha, T.), In ACS Chem Biol, 2018. |
[237] | TGFβ1 reinforces arterial aging in the vascular smooth muscle cell through a long-range regulation of the cytoskeletal stiffness. (), In Sci Rep, 2018. |
[236] | Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution. (Koh, H. R., Roy, R., Sorokina, M., Tang, G. Q., Nandakumar, D., Patel, S. S. and Ha, T.), In Mol Cell, 2018. |
[235] | Single-Molecule Studies of ssDNA-Binding Proteins Exchange. (Yang, O. and Ha, T.), In Methods Enzymol, 2018. |
[234] | Mechanism of polypurine tract primer generation by HIV-1 reverse transcriptase. (Figiel, M., Krepl, M., Park, S., Poznański, J., Skowronek, K., Gołąb, A., Ha, T., Šponer, J. and Nowotny, M.), In J Biol Chem, 2018. |
[233] | Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution. (Fei, J., Jadaliha, M., Harmon, T. S., Li, I. T. S., Hua, B., Hao, Q., Holehouse, A. S., Reyer, M., Sun, Q., Freier, S. M., Pappu, R. V., Prasanth, K. V. and Ha, T.), In J Cell Sci, 2017. |
[232] | Single-cell analysis of early antiviral gene expression reveals a determinant of stochastic IFNB1 expression. (), In Integr Biol (Camb), 2017. |
[231] | Sphingolipids facilitate age asymmetry of membrane proteins in dividing yeast cells. (Singh, P., Ramachandran, S. K., Zhu, J., Kim, B. C., Biswas, D., Ha, T., Iglesias, P. A. and Li, R.), In Mol Biol Cell, 2017. |
[230] | Metals induce transient folding and activation of the twister ribozyme. (Panja, S., Hua, B., Zegarra, D., Ha, T. and Woodson, S. A.), In Nat Chem Biol, 2017. |
[229] | Single-molecule imaging reveals the translocation and DNA looping dynamics of hepatitis C virus NS3 helicase. (Lin, C. T., Tritschler, F., Lee, K. S., Gu, M., Rice, C. M. and Ha, T.), In Protein Sci, 2017. |
[228] | Structural biology: Growth factor rattled out of its cage. (), In Nature, 2017. |
[227] | Probing Single Helicase Dynamics on Long Nucleic Acids Through Fluorescence-Force Measurement. (Lin, C. T. and Ha, T.), In Methods Mol Biol, 2017. |
[226] | A genetically encoded fluorescent tRNA is active in live-cell protein synthesis. (Masuda, I., Igarashi, T., Sakaguchi, R., Nitharwal, R. G., Takase, R., Han, K. Y., Leslie, B. J., Liu, C., Gamper, H., Ha, T., Sanyal, S. and Hou, Y. M.), In Nucleic Acids Res, 2017. |
[225] | Notch-Jagged complex structure implicates a catch bond in tuning ligand sensitivity. (), In Science, 2017. |
[224] | Flipping nanoscopy on its head. (), In Science, 2017. |
[223] | Mapping cell surface adhesion by rotation tracking and adhesion footprinting. (), In Sci Rep, 2017. |
[222] | Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes. (), In Nat Commun, 2017. |
[221] | Voltage-gated sodium channels assemble and gate as dimers. (), In Nat Commun, 2017. |
[220] | Single-Molecule Analysis of Lipid-Protein Interactions in Crude Cell Lysates. (Arauz, E., Aggarwal, V., Jain, A., Ha, T. and Chen, J.), In Anal Chem, 2016. |
[219] | A Chemical Controller of SNARE-Driven Membrane Fusion That Primes Vesicles for Ca(2+)-Triggered Millisecond Exocytosis. (Heo, P., Yang, Y., Han, K. Y., Kong, B., Shin, J. H., Jung, Y., Jeong, C., Shin, J., Shin, Y. K., Ha, T. and Kweon, D. H.), In J Am Chem Soc, 2016. |
[218] | Rupture force of cell adhesion ligand tethers modulates biological activities of a cell-laden hydrogel. (Lee, M. K., Park, J., Wang, X., Roein-Peikar, M., Ko, E., Qin, E., Lee, J., Ha, T. and Kong, H.), In Chem Commun (Camb), 2016. |
[217] | Natural antisense RNA promotes 3' end processing and maturation of MALAT1 lncRNA. (Zong, X., Nakagawa, S., Freier, S. M., Fei, J., Ha, T., Prasanth, S. G. and Prasanth, K. V.), In Nucleic Acids Res, 2016. |
[216] | Plantazolicin is an ultra-narrow spectrum antibiotic that targets the Bacillus anthracis membrane. (), In ACS Infect Dis, 2016. |
[215] | Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation. (), In Nat Commun, 2016. |
[214] | Probing Nature's Nanomachines One Molecule at a Time. (Ha, T.), In Biophys J, 2016. |
[213] | Spider Silk Peptide Is a Compact, Linear Nanospring Ideal for Intracellular Tension Sensing. (Brenner, M. D., Zhou, R., Conway, D. E., Lanzano, L., Gratton, E., Schwartz, M. A. and Ha, T.), In Nano Lett, 2016. |
[212] | The light side of the force. (), In Elife, 2016. |
[211] | Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability. (), In Nat Commun, 2016. |
[210] | Constructing modular and universal single molecule tension sensor using protein G to study mechano-sensitive receptors. (), In Sci Rep, 2016. |
[209] | Structural dynamics of potassium-channel gating revealed by single-molecule FRET. (Wang, S., Vafabakhsh, R., Borschel, W. F., Ha, T. and Nichols, C. G.), In Nat Struct Mol Biol, 2016. |
[208] | Nanoscale mechanics guides cellular decision making. (), In Integr Biol (Camb), 2016. |
[207] | Ebola Virus Does Not Induce Stress Granule Formation during Infection and Sequesters Stress Granule Proteins within Viral Inclusions. (Nelson, E. V., Schmidt, K. M., Deflubé, L. R., Doğanay, S., Banadyga, L., Olejnik, J., Hume, A. J., Ryabchikova, E., Ebihara, H., Kedersha, N., Ha, T. and Mühlberger, E.), In J Virol, 2016. |
[206] | Defining Single Molecular Forces Required for Notch Activation Using Nano Yoyo. (Chowdhury, F., Li, I. T., Ngo, T. T., Leslie, B. J., Kim, B. C., Sokoloski, J. E., Weiland, E., Wang, X., Chemla, Y. R., Lohman, T. M. and Ha, T.), In Nano Lett, 2016. |
[205] | Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9. (), In Nat Commun, 2016. |
[204] | Single-molecule fluorescence microscopy of native macromolecular complexes. (Aggarwal, V. and Ha, T.), In Curr Opin Struct Biol, 2016. |
[203] | Correction: Nanoscale mechanics guides cellular decision making. (), In Integr Biol (Camb), 2016. |
[202] | In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes. (), In Plant Cell, 2016. |
[201] | 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. (Lee, H. R., Mitra, J., Lee, S., Gao, S. J., Oh, T. K., Kim, M. H., Ha, T. and Jung, J. U.), In J Virol, 2016. |
[200] | Effects of DNA replication on mRNA noise. (Peterson, J. R., Cole, J. A., Fei, J., Ha, T. and Luthey-Schulten, Z. A.), In Proc Natl Acad Sci U S A, 2015. |
[199] | Integrin Molecular Tension within Motile Focal Adhesions. (Wang, X., Sun, J., Xu, Q., Chowdhury, F., Roein-Peikar, M., Wang, Y. and Ha, T.), In Biophys J, 2015. |
[198] | Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells. (), In Sci Rep, 2015. |
[197] | Single molecular force across single integrins dictates cell spreading. (), In Integr Biol (Camb), 2015. |
[196] | Allosteric Regulation of E-Cadherin Adhesion. (Shashikanth, N., Petrova, Y. I., Park, S., Chekan, J., Maiden, S., Spano, M., Ha, T., Gumbiner, B. M. and Leckband, D. E.), In J Biol Chem, 2015. |
[195] | BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase. (Khan, A., Giri, S., Wang, Y., Chakraborty, A., Ghosh, A. K., Anantharaman, A., Aggarwal, V., Sathyan, K. M., Ha, T., Prasanth, K. V. and Prasanth, S. G.), In Proc Natl Acad Sci U S A, 2015. |
[194] | Dual-color three-dimensional STED microscopy with a single high-repetition-rate laser. (), In Opt Lett, 2015. |
[193] | A parameter estimation method for fluorescence lifetime data. (), In BMC Res Notes, 2015. |
[192] | Protein structure. Direct observation of structure-function relationship in a nucleic acid-processing enzyme. (), In Science, 2015. |
[191] | The preRC protein ORCA organizes heterochromatin by assembling histone H3 lysine 9 methyltransferases on chromatin. (), In Elife, 2015. |
[190] | Protein structure. Engineering of a superhelicase through conformational control. (), In Science, 2015. |
[189] | Nucleosomes undergo slow spontaneous gaping. (Ngo, T. T. and Ha, T.), In Nucleic Acids Res, 2015. |
[188] | RNA biochemistry. Determination of in vivo target search kinetics of regulatory noncoding RNA. (), In Science, 2015. |
[187] | Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility. (), In Cell, 2015. |
[186] | Distinct mechanisms regulating mechanical force-induced Ca²⁺ signals at the plasma membrane and the ER in human MSCs. (), In Elife, 2015. |
[185] | Dynamic growth and shrinkage govern the pH dependence of RecA filament stability. (Kim, S. H., Park, J., Joo, C., Kim, D. and Ha, T.), In PLoS One, 2015. |
[184] | RNA fluorescence in situ hybridization in cultured mammalian cells. (Tripathi, V., Fei, J., Ha, T. and Prasanth, K. V.), In Methods Mol Biol, 2015. |
[183] | Stoichiometry and assembly of mTOR complexes revealed by single-molecule pulldown. (Jain, A., Arauz, E., Aggarwal, V., Ikon, N., Chen, J. and Ha, T.), In Proc Natl Acad Sci U S A, 2014. |
[182] | A price to pay for relaxed substrate specificity: a comparative kinetic analysis of the class II lanthipeptide synthetases ProcM and HalM2. (Thibodeaux, C. J., Ha, T. and van der Donk, W. A.), In J Am Chem Soc, 2014. |
[181] | An improved surface passivation method for single-molecule studies. (Hua, B., Han, K. Y., Zhou, R., Kim, H., Shi, X., Abeysirigunawardena, S. C., Jain, A., Singh, D., Aggarwal, V., Woodson, S. A. and Ha, T.), In Nat Methods, 2014. |
[180] | Designing a nine cysteine-less DNA packaging motor from bacteriophage T4 reveals new insights into ATPase structure and function. (), In Virology, 2014. |
[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. (), In Bioessays, 2014. |
[178] | Targeting DNA G-quadruplexes with helical small molecules. (), In Chembiochem, 2014. |
[177] | Single-molecule packaging initiation in real time by a viral DNA packaging machine from bacteriophage T4. (Vafabakhsh, R., Kondabagil, K., Earnest, T., Lee, K. S., Zhang, Z., Dai, L., Dahmen, K. A., Rao, V. B. and Ha, T.), In Proc Natl Acad Sci U S A, 2014. |
[176] | Cooperative conformational transitions keep RecA filament active during ATPase cycle. (Kim, S. H., Ragunathan, K., Park, J., Joo, C., Kim, D. and Ha, T.), In J Am Chem Soc, 2014. |
[175] | Single-molecule methods leap ahead. (Ha, T.), In Nat Methods, 2014. |
[174] | Matrix softness regulates plasticity of tumour-repopulating cells via H3K9 demethylation and Sox2 expression. (), In Nat Commun, 2014. |
[173] | A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment. (), In J Chem Theory Comput, 2014. |
[172] | Biophysics. Ultraslow relaxation of confined DNA. (), In Science, 2014. |
[171] | Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer. (Lee, K. S., Marciel, A. B., Kozlov, A. G., Schroeder, C. M., Lohman, T. M. and Ha, T.), In J Mol Biol, 2014. |
[170] | Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA. (), In Elife, 2014. |
[169] | Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA. (Zhang, J., Zhou, R., Inoue, J., Mikawa, T. and Ha, T.), In Nucleic Acids Res, 2014. |
[168] | Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase. (), In Cell Rep, 2014. |
[167] | Dynamic look at DNA unwinding by a replicative helicase. (Lee, S. J., Syed, S., Enemark, E. J., Schuck, S., Stenlund, A., Ha, T. and Joshua-Tor, L.), In Proc Natl Acad Sci U S A, 2014. |
[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. (Lee, H. R., Doğanay, S., Chung, B., Toth, Z., Brulois, K., Lee, S., Kanketayeva, Z., Feng, P., Ha, T. and Jung, J. U.), In J Virol, 2014. |
[165] | Crosstalk between the cGAS DNA sensor and Beclin-1 autophagy protein shapes innate antimicrobial immune responses. (), In Cell Host Microbe, 2014. |
[164] | Protein-guided RNA dynamics during early ribosome assembly. (), In Nature, 2014. |
[163] | Single-molecule optical spectroscopy. (), In Chem Soc Rev, 2014. |
[162] | Structural mechanisms of PriA-mediated DNA replication restart. (Bhattacharyya, B., George, N. P., Thurmes, T. M., Zhou, R., Jani, N., Wessel, S. R., Sandler, S. J., Ha, T. and Keck, J. L.), In Proc Natl Acad Sci U S A, 2014. |
[161] | Towards a computational model of a methane producing archaeum. (), In Archaea, 2014. |
[160] | Relaxed rotational and scrunching changes in P266L mutant of T7 RNA polymerase reduce short abortive RNAs while delaying transition into elongation. (Tang, G. Q., Nandakumar, D., Bandwar, R. P., Lee, K. S., Roy, R., Ha, T. and Patel, S. S.), In PLoS One, 2014. |
[159] | Understanding the photophysics of the spinach-DFHBI RNA aptamer-fluorogen complex to improve live-cell RNA imaging. (Han, K. Y., Leslie, B. J., Fei, J., Zhang, J. and Ha, T.), In J Am Chem Soc, 2013. |
[158] | Watching DNA breath one molecule at a time. (Fei, J. and Ha, T.), In Proc Natl Acad Sci U S A, 2013. |
[157] | ATPase-driven oligomerization of RIG-I on RNA allows optimal activation of type-I interferon. (Patel, J. R., Jain, A., Chou, Y. Y., Baum, A., Ha, T. and García-Sastre, A.), In EMBO Rep, 2013. |
[156] | Molecular mechanism of sequence-dependent stability of RecA filament. (Kim, S. H., Joo, C., Ha, T. and Kim, D.), In Nucleic Acids Res, 2013. |
[155] | Single-molecule approaches embrace molecular cohorts. (), In Cell, 2013. |
[154] | A dendritic single-molecule fluorescent probe that is monovalent, photostable and minimally blinking. (), In Nat Chem, 2013. |
[153] | Single-molecule FRET reveals the native-state dynamics of the IκBα ankyrin repeat domain. (Lamboy, J. A., Kim, H., Dembinski, H., Ha, T. and Komives, E. A.), In J Mol Biol, 2013. |
[152] | PriC-mediated DNA replication restart requires PriC complex formation with the single-stranded DNA-binding protein. (Wessel, S. R., Marceau, A. H., Massoni, S. C., Zhou, R., Ha, T., Sandler, S. J. and Keck, J. L.), In J Biol Chem, 2013. |
[151] | Defining single molecular forces required to activate integrin and notch signaling. (), In Science, 2013. |
[150] | Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation. (), In RNA, 2013. |
[149] | The SOSS1 single-stranded DNA binding complex promotes DNA end resection in concert with Exo1. (Yang, S. H., Zhou, R., Campbell, J., Chen, J., Ha, T. and Paull, T. T.), In EMBO J, 2013. |
[148] | Single-molecule nanometry for biological physics. (), In Rep Prog Phys, 2013. |
[147] | Fusion pore formation and expansion induced by Ca2+ and synaptotagmin 1. (Lai, Y., Diao, J., Liu, Y., Ishitsuka, Y., Su, Z., Schulten, K., Ha, T. and Shin, Y. K.), In Proc Natl Acad Sci U S A, 2013. |
[146] | Direct imaging of single UvrD helicase dynamics on long single-stranded DNA. (), In Nat Commun, 2013. |
[145] | The telomere capping complex CST has an unusual stoichiometry, makes multipartite interaction with G-Tails, and unfolds higher-order G-tail structures. (Lue, N. F., Zhou, R., Chico, L., Mao, N., Steinberg-Neifach, O. and Ha, T.), In PLoS Genet, 2013. |
[144] | Single-molecule FRET with total internal reflection microscopy. (), In Cold Spring Harb Protoc, 2012. |
[143] | Prism-type total internal reflection microscopy for single-molecule FRET. (), In Cold Spring Harb Protoc, 2012. |
[142] | RecA filament sliding on DNA facilitates homology search. (), In Elife, 2012. |
[141] | Activated GTPase movement on an RNA scaffold drives co-translational protein targeting. (), In Nature, 2012. |
[140] | Objective-type total internal reflection microscopy (emission) for single-molecule FRET. (), In Cold Spring Harb Protoc, 2012. |
[139] | Objective-type total internal reflection microscopy (excitation) for single-molecule FRET. (), In Cold Spring Harb Protoc, 2012. |
[138] | Imaging and identifying impurities in single-molecule FRET studies. (), In Cold Spring Harb Protoc, 2012. |
[137] | Preparing sample chambers for single-molecule FRET. (), In Cold Spring Harb Protoc, 2012. |
[136] | A helicase with an extra spring in its step. (), In Cell, 2012. |
[135] | Labeling proteins for single-molecule FRET. (), In Cold Spring Harb Protoc, 2012. |
[134] | Labeling DNA (or RNA) for single-molecule FRET. (), In Cold Spring Harb Protoc, 2012. |
[133] | Dynamics of major histocompatibility complex class I association with the human peptide-loading complex. (Panter, M. S., Jain, A., Leonhardt, R. M., Ha, T. and Cresswell, P.), In J Biol Chem, 2012. |
[132] | Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. (), In Science, 2012. |
[131] | Dynamic association of ORCA with prereplicative complex components regulates DNA replication initiation. (Shen, Z., Chakraborty, A., Jain, A., Giri, S., Ha, T., Prasanth, K. V. and Prasanth, S. G.), In Mol Cell Biol, 2012. |
[130] | The influenza A virus PB2, PA, NP, and M segments play a pivotal role during genome packaging. (Gao, Q., Chou, Y. Y., Doğanay, S., Vafabakhsh, R., Ha, T. and Palese, P.), In J Virol, 2012. |
[129] | Elastic coupling between RNA degradation and unwinding by an exoribonuclease. (), In Science, 2012. |
[128] | Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulations. (), In J Phys Chem B, 2012. |
[127] | Single-molecule imaging: a collagenase pauses before embarking on a killing spree. (Lee, G. and Ha, T.), In Curr Biol, 2012. |
[126] | One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis. (Chou, Y. Y., Vafabakhsh, R., Doğanay, S., Gao, Q., Ha, T. and Palese, P.), In Proc Natl Acad Sci U S A, 2012. |
[125] | A rule of seven in Watson-Crick base-pairing of mismatched sequences. (Cisse, I. I., Kim, H. and Ha, T.), In Nat Struct Mol Biol, 2012. |
[124] | A single vesicle-vesicle fusion assay for in vitro studies of SNAREs and accessory proteins. (), In Nat Protoc, 2012. |
[123] | Quantitative fluorescence labeling of aldehyde-tagged proteins for single-molecule imaging. (Shi, X., Jung, Y., Lin, L. J., Liu, C., Wu, C., Cann, I. K. and Ha, T.), In Nat Methods, 2012. |
[122] | Single-molecule pull-down for studying protein interactions. (), In Nat Protoc, 2012. |
[121] | Opening-closing dynamics of the mitochondrial transcription pre-initiation complex. (Kim, H., Tang, G. Q., Patel, S. S. and Ha, T.), In Nucleic Acids Res, 2012. |
[120] | Single-molecule analysis of SSB dynamics on single-stranded DNA. (Zhou, R. and Ha, T.), In Methods Mol Biol, 2012. |
[119] | Single-molecule views of protein movement on single-stranded DNA. (), In Annu Rev Biophys, 2012. |
[118] | Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging. (), In Annu Rev Phys Chem, 2012. |
[117] | Antiparallel EmrE exports drugs by exchanging between asymmetric structures. (), In Nature, 2011. |
[116] | Detecting intramolecular conformational dynamics of single molecules in short distance range with subnanometer sensitivity. (Zhou, R., Kunzelmann, S., Webb, M. R. and Ha, T.), In Nano Lett, 2011. |
[115] | An entirely specific type I A-kinase anchoring protein that can sequester two molecules of protein kinase A at mitochondria. (Means, C. K., Lygren, B., Langeberg, L. K., Jain, A., Dixon, R. E., Vega, A. L., Gold, M. G., Petrosyan, S., Taylor, S. S., Murphy, A. N., Ha, T., Santana, L. F., Tasken, K. and Scott, J. D.), In Proc Natl Acad Sci U S A, 2011. |
[114] | A single-molecule view of chaperonin cooperativity. (Ha, T. and Myong, S.), In Proc Natl Acad Sci U S A, 2011. |
[113] | Rotations of the 2B sub-domain of E. coli UvrD helicase/translocase coupled to nucleotide and DNA binding. (Jia, H., Korolev, S., Niedziela-Majka, A., Maluf, N. K., Gauss, G. H., Myong, S., Ha, T., Waksman, G. and Lohman, T. M.), In J Mol Biol, 2011. |
[112] | Single-molecule nanopositioning: structural transitions of a helicase-DNA complex during ATP hydrolysis. (Balci, H., Arslan, S., Myong, S., Lohman, T. M. and Ha, T.), In Biophys J, 2011. |
[111] | Real-time observation of strand exchange reaction with high spatiotemporal resolution. (), In Structure, 2011. |
[110] | Monovalent, clickable, uncharged, water-soluble perylenediimide-cored dendrimers for target-specific fluorescent biolabeling. (Yang, S. K., Shi, X., Park, S., Doganay, S., Ha, T. and Zimmerman, S. C.), In J Am Chem Soc, 2011. |
[109] | Tyrosine phosphorylation enhances RAD52-mediated annealing by modulating its DNA binding. (Honda, M., Okuno, Y., Yoo, J., Ha, T. and Spies, M.), In EMBO J, 2011. |
[108] | SSB functions as a sliding platform that migrates on DNA via reptation. (), In Cell, 2011. |
[107] | Visualization of the nanospring dynamics of the IkappaBalpha ankyrin repeat domain in real time. (Lamboy, J. A., Kim, H., Lee, K. S., Ha, T. and Komives, E. A.), In Proc Natl Acad Sci U S A, 2011. |
[106] | Editorial on nanobiology. (), In Phys Chem Chem Phys, 2011. |
[105] | Single-molecule analysis reveals three phases of DNA degradation by an exonuclease. (Lee, G., Yoo, J., Leslie, B. J. and Ha, T.), In Nat Chem Biol, 2011. |
[104] | Forcing a connection: impacts of single-molecule force spectroscopy on in vivo tension sensing. (), In Biopolymers, 2011. |
[103] | Probing cellular protein complexes using single-molecule pull-down. (), In Nature, 2011. |
[102] | Ultrahigh-resolution optical trap with single-fluorophore sensitivity. (Comstock, M. J., Ha, T. and Chemla, Y. R.), In Nat Methods, 2011. |
[101] | Reverse-chaperoning activity of an AAA+ protein. (Liu, C., McKinney, M. C., Chen, Y. H., Earnest, T. M., Shi, X., Lin, L. J., Ishino, Y., Dahmen, K., Cann, I. K. and Ha, T.), In Biophys J, 2011. |
[100] | Seeing a molecular machine self-renew. (Shi, X. and Ha, T.), In Proc Natl Acad Sci U S A, 2011. |
[99] | A promiscuous DNA packaging machine from bacteriophage T4. (Zhang, Z., Kottadiel, V. I., Vafabakhsh, R., Dai, L., Chemla, Y. R., Ha, T. and Rao, V. B.), In PLoS Biol, 2011. |
[98] | Homochirality and the origin of life. Editorial of the PCCP themed issue. (), In Phys Chem Chem Phys, 2011. |
[97] | Temperature-independent porous nanocontainers for single-molecule fluorescence studies. (Ishitsuka, Y., Okumus, B., Arslan, S., Chen, K. H. and Ha, T.), In Anal Chem, 2010. |
[96] | Single-molecule four-color FRET. (Lee, J., Lee, S., Ragunathan, K., Joo, C., Ha, T. and Hohng, S.), In Angew Chem Int Ed Engl, 2010. |
[95] | Reversible and controllable nanolocomotion of an RNA-processing machinery. (Lee, G., Hartung, S., Hopfner, K. P. and Ha, T.), In Nano Lett, 2010. |
[94] | Advances in mass spectrometry for biological science. (), In Phys Chem Chem Phys, 2010. |
[93] | 5'-Single-stranded/duplex DNA junctions are loading sites for E. coli UvrD translocase. (Tomko, E. J., Jia, H., Park, J., Maluf, N. K., Ha, T. and Lohman, T. M.), In EMBO J, 2010. |
[92] | The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. (Trabuco, L. G., Schreiner, E., Eargle, J., Cornish, P., Ha, T., Luthey-Schulten, Z. and Schulten, K.), In J Mol Biol, 2010. |
[91] | Water in biological systems. (), In Phys Chem Chem Phys, 2010. |
[90] | A single-vesicle content mixing assay for SNARE-mediated membrane fusion. (), In Nat Commun, 2010. |
[89] | PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps. (), In Cell, 2010. |
[88] | Measuring mechanical tension across vinculin reveals regulation of focal adhesion dynamics. (), In Nature, 2010. |
[87] | Acidification of the oxygen scavenging system in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe. (Shi, X., Lim, J. and Ha, T.), In Anal Chem, 2010. |
[86] | Insight into helicase mechanism and function revealed through single-molecule approaches. (Yodh, J. G., Schlierf, M. and Ha, T.), In Q Rev Biophys, 2010. |
[85] | Inching over hurdles: how DNA helicases move on crowded lattices. (), In Cell Cycle, 2010. |
[84] | Human Rad52 binds and wraps single-stranded DNA and mediates annealing via two hRad52-ssDNA complexes. (Grimme, J. M., Honda, M., Wright, R., Okuno, Y., Rothenberg, E., Mazin, A. V., Ha, T. and Spies, M.), In Nucleic Acids Res, 2010. |
[83] | A comparative study of multivariate and univariate hidden Markov modelings in time-binned single-molecule FRET data analysis. (), In J Phys Chem B, 2010. |
[82] | Biomolecular structures: from isolated molecules to the cell crowded medium. (), In Phys Chem Chem Phys, 2010. |
[81] | Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine. (), In Biochemistry, 2010. |
[80] | Single-Vesicle Fusion Assay Reveals Munc18-1 Binding to the SNARE Core Is Sufficient for Stimulating Membrane Fusion. (), In ACS Chem Neurosci, 2010. |
[79] | Stepwise translocation of nucleic acid motors. (Myong, S. and Ha, T.), In Curr Opin Struct Biol, 2010. |
[78] | Force-fluorescence spectroscopy at the single-molecule level. (Zhou, R., Schlierf, M. and Ha, T.), In Methods Enzymol, 2010. |
[77] | Single-molecule FRET analysis of helicase functions. (Rothenberg, E. and Ha, T.), In Methods Mol Biol, 2010. |
[76] | Real-time observation of G-quadruplex dynamics using single-molecule FRET microscopy. (Okumus, B. and Ha, T.), In Methods Mol Biol, 2010. |
[75] | Coordinating DNA replication by means of priming loop and differential synthesis rate. (), In Nature, 2009. |
[74] | Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase. (Tang, G. Q., Roy, R., Bandwar, R. P., Ha, T. and Patel, S. S.), In Proc Natl Acad Sci U S A, 2009. |
[73] | SSB protein diffusion on single-stranded DNA stimulates RecA filament formation. (), In Nature, 2009. |
[72] | Single molecule nanocontainers made porous using a bacterial toxin. (Okumus, B., Arslan, S., Fengler, S. M., Myong, S. and Ha, T.), In J Am Chem Soc, 2009. |
[71] | Single-molecule analysis reveals differential effect of ssDNA-binding proteins on DNA translocation by XPD helicase. (Honda, M., Park, J., Pugh, R. A., Ha, T. and Spies, M.), In Mol Cell, 2009. |
[70] | G-quadruplex DNA bound by a synthetic ligand is highly dynamic. (Jena, P. V., Shirude, P. S., Okumus, B., Laxmi-Reddy, K., Godde, F., Huc, I., Balasubramanian, S. and Ha, T.), In J Am Chem Soc, 2009. |
[69] | C2AB: a molecular glue for lipid vesicles with a negatively charged surface. (), In Langmuir, 2009. |
[68] | Fluorescent lifetime trajectories of a single fluorophore reveal reaction intermediates during transcription initiation. (Sorokina, M., Koh, H. R., Patel, S. S. and Ha, T.), In J Am Chem Soc, 2009. |
[67] | Photonics: How nanocrystals lost their blink. (), In Nature, 2009. |
[66] | DNA nanotechnology: a nanomachine goes live. (), In Nat Nanotechnol, 2009. |
[65] | Following movement of the L1 stalk between three functional states in single ribosomes. (Cornish, P. V., Ermolenko, D. N., Staple, D. W., Hoang, L., Hickerson, R. P., Noller, H. F. and Ha, T.), In Proc Natl Acad Sci U S A, 2009. |
[64] | BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiation. (Yodh, J. G., Stevens, B. C., Kanagaraj, R., Janscak, P. and Ha, T.), In EMBO J, 2009. |
[63] | Cytosolic viral sensor RIG-I is a 5'-triphosphate-dependent translocase on double-stranded RNA. (), In Science, 2009. |
[62] | Multimodal optical sensing and analyte specificity using single-walled carbon nanotubes. (), In Nat Nanotechnol, 2009. |
[61] | Human Rad52-mediated homology search and annealing occurs by continuous interactions between overlapping nucleoprotein complexes. (Rothenberg, E., Grimme, J. M., Spies, M. and Ha, T.), In Proc Natl Acad Sci U S A, 2008. |
[60] | Roles of RIG-I N-terminal tandem CARD and splice variant in TRIM25-mediated antiviral signal transduction. (Gack, M. U., Kirchhofer, A., Shin, Y. C., Inn, K. S., Liang, C., Cui, S., Myong, S., Ha, T., Hopfner, K. P. and Jung, J. U.), In Proc Natl Acad Sci U S A, 2008. |
[59] | Engineering of functional replication protein a homologs based on insights into the evolution of oligonucleotide/oligosaccharide-binding folds. (Lin, Y., Lin, L. J., Sriratana, P., Coleman, K., Ha, T., Spies, M. and Cann, I. K.), In J Bacteriol, 2008. |
[58] | Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids. (Iqbal, A., Arslan, S., Okumus, B., Wilson, T. J., Giraud, G., Norman, D. G., Ha, T. and Lilley, D. M.), In Proc Natl Acad Sci U S A, 2008. |
[57] | The SNARE complex from yeast is partially unstructured on the membrane. (), In Structure, 2008. |
[56] | Complexin and Ca2+ stimulate SNARE-mediated membrane fusion. (Yoon, T. Y., Lu, X., Diao, J., Lee, S. M., Ha, T. and Shin, Y. K.), In Nat Struct Mol Biol, 2008. |
[55] | A practical guide to single-molecule FRET. (Roy, R., Hohng, S. and Ha, T.), In Nat Methods, 2008. |
[54] | Spontaneous intersubunit rotation in single ribosomes. (Cornish, P. V., Ermolenko, D. N., Noller, H. F. and Ha, T.), In Mol Cell, 2008. |
[53] | Transcription initiation in a single-subunit RNA polymerase proceeds through DNA scrunching and rotation of the N-terminal subdomains. (Tang, G. Q., Roy, R., Ha, T. and Patel, S. S.), In Mol Cell, 2008. |
[52] | Branch migration enzyme as a Brownian ratchet. (Rasnik, I., Jeong, Y. J., McKinney, S. A., Rajagopal, V., Patel, S. S. and Ha, T.), In EMBO J, 2008. |
[51] | Advances in single-molecule fluorescence methods for molecular biology. (Joo, C., Balci, H., Ishitsuka, Y., Buranachai, C. and Ha, T.), In Annu Rev Biochem, 2008. |
[50] | Dissecting metal ion-dependent folding and catalysis of a single DNAzyme. (Kim, H. K., Rasnik, I., Liu, J., Ha, T. and Lu, Y.), In Nat Chem Biol, 2007. |
[49] | How directional translocation is regulated in a DNA helicase motor. (Yu, J., Ha, T. and Schulten, K.), In Biophys J, 2007. |
[48] | MCM forked substrate specificity involves dynamic interaction with the 5'-tail. (Rothenberg, E., Trakselis, M. A., Bell, S. D. and Ha, T.), In J Biol Chem, 2007. |
[47] | Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction. (), In Science, 2007. |
[46] | Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase. (), In Science, 2007. |
[45] | Fueling protein DNA interactions inside porous nanocontainers. (Cisse, I., Okumus, B., Joo, C. and Ha, T.), In Proc Natl Acad Sci U S A, 2007. |
[44] | Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein. (Roy, R., Kozlov, A. G., Lohman, T. M. and Ha, T.), In J Mol Biol, 2007. |
[43] | Need for speed: mechanical regulation of a replicative helicase. (), In Cell, 2007. |
[42] | Single-molecule conformational analysis of G-quadruplex formation in the promoter DNA duplex of the proto-oncogene c-kit. (Shirude, P. S., Okumus, B., Ying, L., Ha, T. and Balasubramanian, S.), In J Am Chem Soc, 2007. |
[41] | A survey of single-molecule techniques in chemical biology. (Cornish, P. V. and Ha, T.), In ACS Chem Biol, 2007. |
[40] | Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA. (Arluison, V., Hohng, S., Roy, R., Pellegrini, O., Régnier, P. and Ha, T.), In Nucleic Acids Res, 2007. |
[39] | Multiple intermediates in SNARE-induced membrane fusion. (Yoon, T. Y., Okumus, B., Zhang, F., Shin, Y. K. and Ha, T.), In Proc Natl Acad Sci U S A, 2006. |
[38] | Nonblinking and long-lasting single-molecule fluorescence imaging. (Rasnik, I., McKinney, S. A. and Ha, T.), In Nat Methods, 2006. |
[37] | Methanosarcina acetivorans flap endonuclease 1 activity is inhibited by a cognate single-stranded-DNA-binding protein. (Lin, Y., Guzman, C. E., McKinney, M. C., Nair, S. K., Ha, T. and Cann, I. K.), In J Bacteriol, 2006. |
[36] | Structure-based model of the stepping motor of PcrA helicase. (Yu, J., Ha, T. and Schulten, K.), In Biophys J, 2006. |
[35] | Analysis of single-molecule FRET trajectories using hidden Markov modeling. (McKinney, S. A., Joo, C. and Ha, T.), In Biophys J, 2006. |
[34] | Real-time observation of RecA filament dynamics with single monomer resolution. (), In Cell, 2006. |
[33] | Defocused orientation and position imaging (DOPI) of myosin V. (Toprak, E., Enderlein, J., Syed, S., McKinney, S. A., Petschek, R. G., Ha, T., Goldman, Y. E. and Selvin, P. R.), In Proc Natl Acad Sci U S A, 2006. |
[32] | Bridging conformational dynamics and function using single-molecule spectroscopy. (), In Structure, 2006. |
[31] | Single molecule nanometronome. (Buranachai, C., McKinney, S. A. and Ha, T.), In Nano Lett, 2006. |
[30] | RNA folding and the origins of catalytic activity in the hairpin ribozyme. (Wilson, T. J., Nahas, M., Araki, L., Harusawa, S., Ha, T. and Lilley, D. M.), In Blood Cells Mol Dis, 2006. |
[29] | Unraveling helicase mechanisms one molecule at a time. (Rasnik, I., Myong, S. and Ha, T.), In Nucleic Acids Res, 2006. |
[28] | Extreme conformational diversity in human telomeric DNA. (Lee, J. Y., Okumus, B., Kim, D. S. and Ha, T.), In Proc Natl Acad Sci U S A, 2005. |
[27] | Repetitive shuttling of a motor protein on DNA. (), In Nature, 2005. |
[26] | Surfaces and orientations: much to FRET about? (Rasnik, I., McKinney, S. A. and Ha, T.), In Acc Chem Res, 2005. |
[25] | Interhead distance measurements in myosin VI via SHRImP support a simplified hand-over-hand model. (Balci, H., Ha, T., Sweeney, H. L. and Selvin, P. R.), In Biophys J, 2005. |
[24] | Single-molecule quantum-dot fluorescence resonance energy transfer. (), In Chemphyschem, 2005. |
[23] | Observing spontaneous branch migration of Holliday junctions one step at a time. (McKinney, S. A., Freeman, A. D., Lilley, D. M. and Ha, T.), In Proc Natl Acad Sci U S A, 2005. |
[22] | The euryarchaeota, nature's medium for engineering of single-stranded DNA-binding proteins. (Robbins, J. B., McKinney, M. C., Guzman, C. E., Sriratana, B., Fitz-Gibbon, S., Ha, T. and Cann, I. K.), In J Biol Chem, 2005. |
[21] | Stereospecific effects determine the structure of a four-way DNA junction. (Liu, J., Déclais, A. C., McKinney, S. A., Ha, T., Norman, D. G. and Lilley, D. M.), In Chem Biol, 2005. |
[20] | Observation of internal cleavage and ligation reactions of a ribozyme. (Nahas, M. K., Wilson, T. J., Hohng, S., Jarvie, K., Lilley, D. M. and Ha, T.), In Nat Struct Mol Biol, 2004. |
[19] | Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic. (Okumus, B., Wilson, T. J., Lilley, D. M. and Ha, T.), In Biophys J, 2004. |
[18] | Exploring rare conformational species and ionic effects in DNA Holliday junctions using single-molecule spectroscopy. (Joo, C., McKinney, S. A., Lilley, D. M. and Ha, T.), In J Mol Biol, 2004. |
[17] | Single-molecule three-color FRET. (Hohng, S., Joo, C. and Ha, T.), In Biophys J, 2004. |
[16] | Structural dynamics and processing of nucleic acids revealed by single-molecule spectroscopy. (), In Biochemistry, 2004. |
[15] | Single-molecule high-resolution imaging with photobleaching. (Gordon, M. P., Ha, T. and Selvin, P. R.), In Proc Natl Acad Sci U S A, 2004. |
[14] | Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy. (Murphy, M. C., Rasnik, I., Cheng, W., Lohman, T. M. and Ha, T.), In Biophys J, 2004. |
[13] | Conformational flexibility of four-way junctions in RNA. (Hohng, S., Wilson, T. J., Tan, E., Clegg, R. M., Lilley, D. M. and Ha, T.), In J Mol Biol, 2004. |
[12] | Functional analysis of multiple single-stranded DNA-binding proteins from Methanosarcina acetivorans and their effects on DNA synthesis by DNA polymerase BI. (Robbins, J. B., Murphy, M. C., White, B. A., Mackie, R. I., Ha, T. and Cann, I. K.), In J Biol Chem, 2004. |
[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. (Rasnik, I., Myong, S., Cheng, W., Lohman, T. M. and Ha, T.), In J Mol Biol, 2004. |
[10] | Near-complete suppression of quantum dot blinking in ambient conditions. (Hohng, S. and Ha, T.), In J Am Chem Soc, 2004. |
[9] | Discrete and heterogeneous rotational dynamics of single membrane probe dyes in gel phase supported lipid bilayer. (), In J Chem Phys, 2004. |
[8] | Conformational model of the Holliday junction transition deduced from molecular dynamics simulations. (Yu, J., Ha, T. and Schulten, K.), In Nucleic Acids Res, 2004. |
[7] | A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. (Tan, E., Wilson, T. J., Nahas, M. K., Clegg, R. M., Lilley, D. M. and Ha, T.), In Proc Natl Acad Sci U S A, 2003. |
[6] | Photodestruction intermediates probed by an adjacent reporter molecule. (Ha, T. and Xu, J.), In Phys Rev Lett, 2003. |
[5] | Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization. (), In Science, 2003. |
[4] | Structural dynamics of individual Holliday junctions. (McKinney, S. A., Déclais, A. C., Lilley, D. M. and Ha, T.), In Nat Struct Biol, 2003. |
[3] | Early steps of supported bilayer formation probed by single vesicle fluorescence assays. (Johnson, J. M., Ha, T., Chu, S. and Boxer, S. G.), In Biophys J, 2002. |
[2] | Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase. (), In Nature, 2002. |
[1] | Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. (Kim, H. D., Nienhaus, G. U., Ha, T., Orr, J. W., Williamson, J. R. and Chu, S.), In Proc Natl Acad Sci U S A, 2002. |