Publications
Preprints
Sina Jazani, Taekjip Ha
Single molecule studies of the native hair cell mechanosensory transduction complex
Sarah Clark, Jaba Mitra, Johannes Elferich, April Goehring, Jingpeng Ge, Taekjip Ha, Eric Gouaux
bioRxiv 2023.12.11.571162; doi: https://doi.org/10.1101/2023.12.11.571162
GAGA Factor Overcomes 1D Diffusion Barrier by 3D Diffusion in Search of Nucleosomal Targets
Xinyu A. Feng, Kaitlin M. Ness, Celina Liu, Ishtiyaq Ahmed, Gregory D. Bowman, Taekjip Ha, Carl Wu
bioRxiv 2023.07.14.549009; doi: https://doi.org/10.1101/2023.07.14.549009
Dynamin 1xA interacts with Endophilin A1 via its spliced long C-terminus for ultrafast endocytosis
Yuuta Imoto, Jing Xue, Lin Luo, Sumana Raychaudhuri, Kie Itoh, Ye Ma, George E. Craft, Ann H. Kwan, Joel P. Mackay, Taekjip Ha, Shigeki Watanabe, Phillip J. Robinson
bioRxiv 2023.09.21.558797; doi: https://doi.org/10.1101/2023.09.21.558797
BuGZ exhibits guanine nucleotide exchange factor activity toward tubulin
Wesley J. Yon, Joseph R. Tran, Taekjip Ha, Yixian Zheng, Ross T.A. Pedersen
bioRxiv 2023.05.09.539990; doi: https://doi.org/10.1101/2023.05.09.539990
Electrostatic encoding of genome organization principles within single native nucleosomes
Sangwoo Park, Advait Athreya, Gustavo Ezequiel Carrizo, Nils A. Benning, Michelle M. Mitchener, Natarajan V. Bhanu, Benjamin A. Garcia, Bin Zhang, Tom W. Muir, Erika L. Pearce, Taekjip Ha
bioRxiv 2023.12.08.570828; doi: https://doi.org/10.1101/2023.12.08.570828
Massively parallel single molecule tracking of sequence-dependent DNA mismatch repair in vivo
Tunc Kayikcioglu, Jasmin S. Zarb, Sonisilpa Mohapatra, Chang-Ting Lin, James A. London, Kasper D. Hansen, Richard Fishel, Taekjip Ha
bioRxiv 2023.01.08.523062; doi: https://doi.org/10.1101/2023.01.08.523062
Dynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin Remodelers
Jee Min Kim, Claudia C. Carcamo, Sina Jazani, Zepei Xie, Xinyu A. Feng, Matthew Poyton, Katie L. Holland, Jonathan B. Grimm, Luke D. Lavis, Taekjip Ha, Carl Wu
bioRxiv 2023.06.13.544671; doi: https://doi.org/10.1101/2023.06.13.544671
The repeat region of the circumsporozoite protein is an elastic linear spring with a functional role in Plasmodium sporozoite motility
Amanda E. Balaban, Sachie Kanatani, Jaba Mitra, Jason Gregory, Natasha Vartak, Ariadne Sinnis-Bourozikas, Fredrich Frischknecht, Taekjip Ha, Photini Sinnis
bioRxiv 2021.05.12.443759; doi: https://doi.org/10.1101/2021.05.12.443759
2024
S. Pangeni, Gargi Biswas, Vikas Kaushik, Sahiti Kuppa, Olivia Yang, Chang-Ting Lin, Garima Mishra, Yaakov Levy, Edwin Antony, Taekjip Ha, "Rapid long-distance migration of RPA on single stranded DNA occurs through intersegmental transfer utilizing multivalent interactions", J. Mol. Biol. 13:168491 (2024) (📄pdf).
Thuy T. M. Ngo, Bailey Liu, Feng Wang, Aakash Basu, Carl Wu, Taekjip Ha, "Dependence of Nucleosome Mechanical Stability on DNA Mismatches" eLife, 13:RP95514 (2024) https://doi.org/10.7554/eLife.95514.1
M.H. Jo, P. Meneses, O. Yang, C. C. Carcamo, S. Pangeni and T. Ha, “Determination of single molecule loading rate during mechanotransduction in cell adhesion” Science 383, 1374-1379 (2024). (full text link) (📄pdf).
J.M. Kim, C.C. Carcamo, S. Jazani, Z. Xie, X.A. Feng, M. Yamadi, M. Poyton, K.L. Holland, J.B. Grimm, L.D. Lavis, T. Ha and C. Wu, “Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers”, eLife 12:RP9143 (2024) (📄 pdf).
T. Ha, J. Fei, S. Schmid, N.K. Lee, R.L. Gonzalez Jr., S. Paul and S. Yeou, “Fluorescence resonance energy transfer at the single-molecule level”, Nature Reviews Methods Primers (2024) (📄 pdf).
M. Gavrilov, J. Zhang, O. Yang and T. Ha, “Free-energy measuring nanopore device”, Physical Review E 109, 024404 (2024) (📄 pdf).
S. Rudnizky, P. J. Murray, C. H. Wolfe and T. Ha, “Single Macromolecule Studies of Eukaryotic Genome Maintenance”, Annual Review of Physical Chemistry (2024) (📄 pdf).
J. Li*, M.H. Jo*, J. Yan, T. Hall, J. Lee, U. Lopez-Sanchez, S. Yan, T. Ha** and T.A. Springer**, “Ligand binding initiates single molecule integrin conformational activation” Cell (in press).
2023
I. Okafor and T. Ha, “Single molecule FRET analysis of CRISPR Cas9 single guide RNA folding dynamics”, Journal of Physical Chemistry B 127, 45-51(2023) (📄 pdf).
I. Aifuwa, B.C. Kim, P. Kamat, B. Starich, A. Agrawal, D. Tanrioven, T. R. Luperchio, A. M. Jimenez Valencia, T. Perestrelo, K. Reddy, T. Ha and J.M. Philip, “Senescent stroma induces nuclear deformations in cancer cells via the inhibition of RhoA/ROCK/myosin II-based cytoskeletal tension”, PNAS Nexus, 2, pgac270 (2023) (📄 pdf).
G. Agam, C. Gebhardt, M. Popara, R. Mächtel, J. Folz, B. Ambrose, N. Chamachi, S. Y. Chung, T. D. Craggs, M. de Boer, D. Grohmann, T. Ha, A. Hartmann, J. Hendrix, V. Hirschfeld, C. G. Hübner, T. Hugel, D. Kammerer, H -S. Kang, A. N. Kapanidis, G. Krainer, K. Kramm, E. A. Lemke, E. Lerner, E. Margeat, K. Martens, J. Michaelis, J. Mitra, G. G. M. Muñoz, R. B. Quast, N. B. Robb, M. Sattler, M. Schlierf, J. Schneider, T. Schröder, A. Sefer, P. S. Tan, J. Thurn, P. Tinnefeld, J. van Noort, S. Weiss, N. Wendler, N. Zijlstra, A. Barth, C. A. M. Seidel, D. C. Lamb and T. Cordes, “Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins”, Nature Methods 20, 523-535 (2023) (📄 pdf).
M. Serey-Gaut, M. Cortes, P. Makrythanasis, M. Suri, A. Taylor, J. Sullivan, A. N. Asleh, J. Mitra, M. A. Dar, A. McNamar, V. Shashi, S. Dugan, X. Song, J. A. Rosenfeld, C. Cabrol, J. Iwaszkiewicz, V. Zoete, D. Pehlivan, Z. C. Akdemir, E. R. Roeder, R. O. Littlejohn, H. Dibra, P. Byrd, G. Stewart, B. B. Geckinli, J. Posey, R. Westman, C. Jungbluth, J. Eason, R. Sachdev, C.-A. Evans, G. Lemire, G. E. VanNoy, A. O’Donnell-Luria, F. T. Mau-Them, A. Juven, J. Piard, C. Y. Nixon, Y. Zhu, T. Ha, Mi. F. Buckley, C. Thauvin, G. K. Essien-Umanah, L. Van Maldergem, J. R. Lupski, T. Roscioli, V. L. Dawson, T. M. Dawson and S. E. Antonarakis, “Biallelic TTI1 variants cause an autosomal recessive neurodevelopmental disorder with microcephaly” American Journal of Human Genetics 110, 499-515 (2023) (📄 pdf).
R. S. Zou, Y. Liu, O. Reyes-Galdo, M. F. Konig, B. K. Mog, L. L. Shen, F. Aviles-Vazquez, A. Marin-Gonzalez and T. Ha, “Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq+”, Nature Methods 20, 706-713 (2023) (📄 pdf).
Y-H. Kim, N. Kim, I. Okafor, S. Choi, S. Min, J. Lee, S. M. Bae, K. Choi, J. Choi, V. Harihar, Y. Kim, B.B. Kleinstiver, J-S. Kim, J.K. Lee, T. Ha & H. H. Kim, “Sniper2L, a high-fidelity Cas9 variant with high activity” Nature Chemical Biology 19, 972-980 (2023) (📄 pdf).
A. Husbands, A. Feller, V. Aggarwal, C. E. Dresden, A. S. Holub, T. Ha and M.C.P. Timmermans, “The START domain potentiates HD-ZIPIII transcriptional activity” Plant Cell 35, 2332-2348 (2023) (📄 pdf).
Y.C. Lin, D. Liu, A. Chakraborty, V. Macias, E. Brister, J. Sonalkar, L. Shen, J. Mitra, T. Ha, A. Kajdacsy-Balla, K. Prasanth & S. Prasanth, “DNA damage-induced S-phase specific phosphorylation of Orc6 is critical for the maintenance of genome stability”, Molecular and Cellular Biology 43, 143-156 (2023) (📄 pdf).
N. Benning, J. Kaeligstel-Hansen, F. Rashid, S. Park, R. Merino Urteaga, T.W. Liao, J. Hao, J. M. Berger, N. Hatzakis & T. Ha, “Dimensional Reduction for Single Molecule Imaging of DNA and Nucleosome Condensation by polyamines, HP1 and Ki-67”, Journal of Physical Chemistry B 127, 1922-1931 (2023) (📄 pdf).
T. Ogunmowo, H. Jing, S. Raychaudhuri, G.F. Kusick, Y. Imoto, S. Li, K. Itoh, Y. Ma, H. Jafri, M. B. Dalva, E.R. Chapman, T. Ha, S. Watanabe and J. Liu, “Membrane compression by synaptic vesicle exocytosis triggers ultrafast endocytosis” Nature Communications 14:2888 (2023) (📄 pdf).
N. M. Livingston, J. Kwon, O. Valera, J. A. Saba, N. K. Sinha, P. Reddy, B. Nelson, C. Wolfe, T. Ha, R. Green, J. Liu and B. Wu, “Bursting translation on single mRNA in live cells”, Molecular Cell 83, 2276-2289 (2023) (📄 pdf).
Y. Liu, W.T. Cottle and T. Ha, “Mapping the dynamics of DNA repair with emerging CRISPR technologies”, Trends in Genetics 39, P560-574 (2023) (📄 pdf).
T.-W. Liao, L. Huang, T.J. Wilson, L. Ganser, D.M.J. Lilley and T. Ha, “Linking folding dynamics and function of SAM/SAH riboswitch at the single molecule level”, Nucleic Acids Research 51, 8957-8969 (2023) (📄 pdf).
R. A. Deshpande, A. Marin-Gonzalez, H. K. Barnes, P. R. Woolley, T. Ha and T. T. Paull, “Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice” Nature Communications 14:5759 (2023) (📄 pdf).
R. Merino-Urteaga and T. Ha, “Mind your tag in single molecule measurements”, Cell Reports Methods 3:100623 (2023) (📄 pdf).
H. Hall-Thomsen, S. Small, M. Gavrilov, T. Ha, R. Schulman and P. Moerman, “Direct uphill strand displacement with an engineered super-helicase”, ACS Synthetic Biology 12, 3424-3432 (2023) (📄 pdf).
M. R. Khan, X. Yin, S. U. Kang, J. Mitra, H. Wang, T. Ryu, S. Brahmachari, S. S. Karuppagounder, Y. Kimura, A. Jhaldiyal, H. H. Kim, H. Gu, R. Chen, J. Redding-Ochoa, J. Troncoso, C. H. Na, T. Ha, V. L. Dawson and T. M Dawson, “Enhanced mTORC1 signaling and protein synthesis in pathologic α-synuclein cellular and animal models of Parkinson’s disease” Science Translational Medicine 15, eadd0499 (2023) (📄 pdf).
D. Bobrovnikov, M. Makurath, C. H. Wolfe, Y. R. Chemla and T. Ha, “Helicase activity modulation with on-demand light-based conformational control” J. Amer. Chem. Soc. 145, 21253-21262 (2023) (📄 pdf).
R.S. Helms, A. Marin-Gonzalez, C.H. Patel, I.H. Sun, J. Wen, R.D. Leone, B. Duvall, R.D. Gao, T. Ha, T. Tsukamoto, B.S. Slusher, J.L. Pomerantz and J.D. Powell, “SIKs regulate HDAC7 stabilization and cytokine recall in late-stage T -cell effector differentiation” J. Immunology 122, 1767-1782 (2023) (📄 pdf).
2022
M. Pittman, E. Iu , K. Li, M. Wang, J. Chen, N. Taneja, M. H. Jo, S. Park, W. H. Jung, L. Liang, I. Barman, T. Ha, S. Gaitanaros, J. Liu, D. Burnette, S. Plotnikov and Y. Chen, “Membrane Ruffling is a Mechanosensor of Extracellular Fluid Viscosity” Nature Physics 18, 1112–1121 (2022) (📄 pdf).
T. Ha, C. Kaiser, S. Myong, B. Wu and J. Xiao, “Next Generation Single Molecule Techniques: Imaging, Labeling and Manipulation in vitro and in cellulo”, Molecular Cell 82, 304-314 (2022) (📄 pdf).
M.F. Poyton, X.A. Feng, A. Ranjan, Q. Lei, F. Wang, J. S. Zarb, R. K. Louder, G. Park. M.H. Jo, J. Ye, S. Liu, T. Ha and C. Wu, “Coordinated DNA and Histone Dynamics Drive Accurate Histone H2A.Z Exchange” Science Advances 8, eabj5509 (2022) (📄 pdf).
R. S. Zou, M. Gavrilov, Y. Liu, D. Rasoloson, M. Conte, J. P. Hardick, L. Shen, S. Chen, A. Pekosz, G. Seydoux, Y.C. Manabe and T. Ha, “Improving the specificity of nucleic acid detection with endonuclease-actuated degradation”, Communications Biology 5:290 (2022) (📄 pdf).
A. Laszlo, J. Craig, M. Gavrilov, R. Tippana, I. Nova, J. Huang, H. Kim, S. Abell, M. deCampos-Sairiker, J. Mount, Jonathan; J. Bowman, K. Baker, H. Higinbotham, D. Bobrovnikov, T. Ha and J. Gundlach, “Sequence-dependent mechanochemical coupling of helicase translocation and unwinding at single-nucleotide resolution”, PNAS 119, e2202489119 (2022).
P. Moerman, M. Gavrilov, T. Ha and R. Schulman, “Catalytic DNA polymerization can be expedited by active product release” Angewandte Chemie e202114581 (2022).
S. Kuppa, J. Deveryshetty, R. Chadda, J. Mattice, N. Pokhrel, V. Kaushik, A. Patterson, N. Dhingra, S. Pangeni, M. K. Sadauskas, S. Shiekh, H. Balci, T. Ha, X. Zhao, B. Bothner and E. Antony, “Rtt105 regulates RNA function by configurationally stapling the flexible domains” Nature Communications 13:5152 (2022).
C. C. Carcamo, M. F. Poyton, A. Rajan, G. Park, R. K. Louder, Feng, X. A., Kim, J. M., T. Dzu, C. Wu and T. Ha, “ATP binding facilitates target search SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA” eLife 11, e77352 (2022).
T. Paul, P. L. Opresko, T. Ha and S. Myong, “Vectorial folding of telomere overhangs promotes higher accessibility”, Nucleic Acids Research 50, 6271-6283 (2022).
Y.C. Lin, A. Chakraborty, J. Mitra, R. Hsu, M. K. Arif, S. Adusumilli, T. Ha, K. Prasanth, and S. Prasanth, “Orc6 is a component of the replication fork and enables efficient mismatch repair” PNAS 119, e2121406119 (2022).
Y. Imoto, S. Raychaudhuri, Y. Ma, P. Fenske, E. Sandoval, K. Itoh, E-M. Blumrich, H. Matsubayashi, L. Mamer, F. Zarebidaki, B. Sohl-Kielczynski, T. Trimbuch, S. Nayak, J. H. Iwasa, J. Liu, B. Wu, T. Ha, T. Inoue, E. M. Jorgensen, M. A. Cousin, C. Rosenmund and S. Watanabe, “Dynamic condensates are primed at endocytic sites for ultrafast endocytosis” Neuron 110, 2815-2835 (2022).
H. Moghimianavval, C. Patel, S. Mohapatra, S.W. Hwang, T. Kayikcioglu, Y. Bashirzadeh, A.P. Liu and T. Ha, “Engineering functional membrane-membrane interface by InterSpy” Small 26:e2202104 (2022).
G. K. E. Umanah, L. Abalde-Atristain, M. R. Kahn, J. Mitra, M. A Dar, M. Chang, K. Tangella, A. McNamara, S. Bennett, R. Chen, V. Aggarwal, M. Cortes, P. Worley, T. Ha, T. D. Dawson and V. L. Dawson, “AAA+ ATPase Thorase inhibits mTOR signaling through the disassembly of the mTOR complex 1”, Nature Communications 13:4836 (2022).
V. A. Morikis, J. Madigan, M. H. Jo, S. J. Chen, L. C. Werba, T. Ha, S. I. Simon, “β2-integrin adhesive bond tension under shear stress modulates cytosolic calcium flux and neutrophil inflammatory response”, Cells 11, 1822 (2022).
R. S. Zou, A. Marin-Gonzalez, Y. Liu, H. B. Liu, L. Shen, R. Dveirin, J.X.J. Luo, R. Kalhor and T. Ha, “Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites” Nature Cell Biology 24, 1433-1444 (2022).
M. Gavrilov, J.Y.C. Yang, R. S. Zou, W. Ma, C.Y. Lee, S. Mohapatra, J. Kang, T.W. Liao, S. Myong and T. Ha, “Engineered helicase eliminates thermocycler from DNA amplification while retaining desired PCR characteristics” Nature Communications 13:6312 (2022).
M.H. Jo, J. Li, V. Jaumouille, Y. Hao, J. Coppola, J. Yan, C.M. Waterman, T.A. Springer and T. Ha, “Single molecule characterization of subtype-specific β1 integrin mechanics”, Nature Communications 13:1471 (2022).
A. Basu, D. Bobrovnikov, B. Cieza, J. P. Arcon, Z. Qureshi, M. Orozco and T. Ha, “Deciphering the mechanical code of the genome and epigenome” Nature Struct. Mol. Bio. 29, 1178-1187 (2022).
Y. Wang. W. T. Cottle, H. Wang, M. Gavrilov, R. S. Zou, M-T. Pham, S. Yegnasubramanian, S. Bailey and T. Ha, “Achieving single nucleotide sensitivity in direct hybridization genome imaging”, Nature Communications, 13, 7776 (2022).
2021
A. Basu, D.G. Bobrovnikov, Z. Qureshi, T. Kayikcioglu, T.T.M. Ngo, A. Ranjan, S. Eustermann, B. Cieza, M.T. Morgan, M. Hejna, H.T. Rube, K.P. Hopfner, C. Wolberger, J.S. Song and T. Ha, “Measuring DNA mechanics on the genome scale” Nature 589, 462-467 (2021).
R. S. Zou, Y. Liu, B. Wu and T. Ha, “Cas9 deactivation with photocleavable guide RNAs”, Molecular Cell 81:1553-1565 (2021).
B. Talluri, K. Aamr, M. Saul, T. Shireen, V. Konjufca, J. Ma, T. Ha and F. Chowdhury, “COL2A1 is a novel biomarker of melanoma tumor repopulating cells”, Biomedicine 8, 360 (2020).
L. Huang, T.W. Liao, J. Wang, T. Ha, and D.M.J. Lilley, “Crystal structure and ligand-induced folding of the SAM/SAH riboswitch”, Nucleic Acids Research 48, 7545-7556 (2020).
B. Hua, C. P. Jones, J. Mitra, P. J. Murray, R. Rosenthal, A. R. Ferre-D’Amare and T. Ha, “Real-time monitoring of single ZTP riboswitches reveals a complex and kinetically controlled decision landscape”, Nature Communications 11, 4531 (2020).
T. Tran, J. Mitra, T. Ha and J.M. Kavran, “Increasing proximity promotes MST2 autophosphorylation during Hippo signaling” J Biol Chem 295, 16166-16179 (2020).
D.M. Bianchi, T.A. Brier, A. Poddar, M.S. Azam, C.K. Vanderpool, T. Ha and Z. Luthey-Schulten, “Stochastic analysis probes the role of the chaperone Hfq in E. coli sugar shock response”, Frontiers in Molecular Biosciences 7:593826 (2020).
G. Zhen, Q. Guo, Y. Li, C. Wu, S. Zhu, R. Wang, E. Guo, B.C. Kim, J. Huang, Y. Hu, Y. Dan, M. Wan, T. Ha, S. An and X. Cao, “Mechanical stress determines the configuration of TGFβ activation in articular cartilage”, Nature Communications 12:1706 (2021).
A. Poddar, M.S. Azam, T. Kayikcioglu, M. Bobrovskyy, J. Zhang, X. Ma, P. Labhsetwar, J. Fei, D. Singh, Z. Luthey-Schulten, C.K. Vanderpool and T. Ha, “Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA”, Nature Communications, 12:874 (2021).
Y. Wang, J. Mallon, H. Wang, D. Singh, M. H. Jo, B. Hua, S. Bailey and T. Ha, “Real-time observation of Cas9 post-catalytic domain motions”, PNAS 118:e2010650118 (2021).
Y. Wang, W.T. Cottle, H. Wang, X.A. Feng, J. Mallon, M. Gavrilov, S. Bailey and T. Ha, “Genome Oligopaint via Local Denaturing Fluorescence In situ Hybridization”, Molecular Cell 81:1566-1577 (2021).
J. Yoo, S. Park, C. Maffeo, T. Ha and A. Aksimentiev, “DNA Sequence and Methylation Prescribe the Inside-Out Conformational Dynamics and Bending Energetics of DNA Minicircles” Nucleic Acids Research 49:11459-11475 (2021).
J. Yu, P. Rao, S. Clark, J. Mitra, T. Ha and E. Gouaux, “Hippocampal AMPA receptor-auxiliary subunit structures and mechanism of allosteric inhibition” Nature 594, 448-453 (2021).
A. Basu and T. Ha, “DNA mechanics and its impact on biological processes”, J. Mol. Biol. 433:166861 (2021).
M.H. Jo, B.C. Kim, K. Sung, R.A. Panettieri, S.S. An, J. Liu and T. Ha, “Molecular nanomechanical mapping of histamine-induced smooth muscle cell contraction and shortening” ACS Nano 15, 11585–11596 (2021).
X. A. Feng, M. F. Poyton and T. Ha, “Multiple color single molecule FRET for DNA and RNA processes”, Current Opinion in Structural Biology 70, 26-33 (2021).
T. Paul, T. Ha and S. Myong “Regeneration of PEG slide for multiple rounds of single-molecule measurements”, Biophysical Journal 120, 1788-1799 (2021).
E. Lerner, A. Barth, J. Hendrix, B. Ambrose, V. Birkedal, S.C. Blanchard, R. Borner, H.S. Chung, T. Cordes, T.D. Craggs, A.A. Deniz, J. Diao, J. Fei, R.L. Gonzalez, I.V. Gopich, T. Ha, C.A. Hanke, G. Haran, N.S. Hatzakis, S. Hohng, S.C. Hong, T. Hugel, A. Ingargiola, C. Joo, A.N. Kapanidis, H.D. Kim, T. Laurence, N.K. Lee, T.H. Lee, E.A. Lemke, E. Margeat, J. Michaelis, X. Michalet, S. Myong, D. Nettels, T.O. Peulen, E. Ploetz, Y. Razvag, N.C. Robb, B. Schuler, H. Soleimaninejad, C. Tang, R. Vafabakhsh, D.C. Lamb, C.A. Seidel and S. Weiss, “FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices”, eLife, 10:e60416 (2021).
L. Dai, D. Singh, S. Lu, V. Kottadiel, R. Vafabakhsh, M. Mahalingam, Y.R. Chemla, T. Ha and V. Rao, “A viral genome packaging ring-ATPase is a flexibly coordinated pentamer” Nature Communications 12:6546 (2021).
N. Singh, A. Reyes-Ordonez, M.A. Compagnone, J.F. Moreno-Castillo, B.J. Leslie, T. Ha and J. Chen, “Redefining the specificity of phosphoinositide-binding by human PH domain-containing proteins”, Nature Communications 12:4339 (2021).
2020
S. Mohapatra, C. T. Lin, X. A. Feng, A. Basu and T. Ha, “Single molecule analysis and engineering of DNA motors” Chemical Reviews 120, 36-78, (2020).
M. Bobrovskyy, J. Frandsen, J. Zhang, A. Poddar, M. S. Azam, T. M. Henkin, T. Ha and C. K. Vanderpool, “Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS”, Molecular Microbiology 112, 1198-1218 (2019).
Y. Liu, R. S. Zou, S. He, Y. Nihongaki, X. Li, S. Razavi, B. Wu and T. Ha, “Very fast CRISPR on demand”, Science 368, 1265–1269 (2020).
N. Su, A. K. Byrd, S. R. Bharath, O. Yang, Y. Jia, X. Tang, T. Ha, K. D. Raney and H. Song, “Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases”, Nature Communications 10:5375 (2019).
A. Korman, H. Sun, B. Hua, H. Yang, J. N. Capilato, R. Paul, S. Panja, T. Ha, M. M. Greenberg and S.A. Woodson, “Light-controlled twister ribozyme with single molecule detection resolves RNA function in time and space”, PNAS, 117, 12080-12086 (2020).
A.D. Gitler, J. Shorter, T. Ha and S. Myong, “Just Took a DNA Test, Turns Out 100% Not That Phase”, Molecular Cell, 78, 193-194 (2020).
R. Hsu, Y. C. Lin, D. Singh, Y. Wang, V. Aggarwal, J. Mitra, A. Matur, T. Ha, K. Prasanth and S. Prasanth, "ORCA/LRWD1 regulates homologous recombination at ALT-telomeres by modulating heterochromatin organization ", iScience 23, 101038 (2020).
S. Park. Y. Shi, B.C. Kim, M.H. Jo, L. Cruz, Z. Gou, T. Ha, L.F. Lu, D. Reich and Y. Chen, "Force-Dependent Trans-endocytosis by Breast Cancer Cells Depletes Costimulatory Receptor CD80 and Attenuates T Cell Activation", Biosensors and Bioelectronics 165, 112389 (2020).
T. Paul, A. Voter, R. Cuny, M. Gavrilov, T. Ha, J. Keck and S. Myong, “E. coli Rep helicase and RecA recombinase unwind G4 DNA and are important for resistance to G4-stabilizing ligands” Nucleic Acids Research 48, 6640-6653 (2020)
K. Rhine, M. A. Makurath, J. Liu, S. Skanchy, C. Lopez, K. F. Catalan, Y. Ma, C.M. Fair, J. Shorter, T. Ha, Y.R. Chemla and S. Myong, “ALS/FTLD-linked mutations in FUS glycine residues cause accelerated gelation and reduced interactions with wild-type FUS”, Molecular Cell 80, 666-681 (2020).
2019
K. Geiger-Schuller, J. Mitra, T. Ha and D. Barrick, “Conformational heterogeneity allows access to DNA in longer transcription activator-like effect (TALE) arrays”, eLife 8:e38298 (2019).
K.Y. Han and T. Ha, “Measuring molecular mass with light”, Nature Photonics 12, 380-381 (2018).
J. Kim, N. Khana, K. Y. Han, T. Ha and A. S. Belmont, “Nuclear speckle fusion via long-range directional motion regulates the number and size of speckles” J. Cell Sci. 132: jcs226563 (2019).
R. Zhou, O. Yang, A.C. Declais, H. Jin, G.H. Gwon, A.D.J. Freeman, Y. Cho, D.M.J. Lilley and T. Ha, “Junction resolving enzymes use multivalent interaction to keep the Holliday junction dynamic” Nat. Chem. Biol. 15, 269-275 (2019).
M. Schlierf, G. Wang, X. S. Chen and T. Ha, “Hexameric helicase G40P unwinds DNA in single base pair steps”, eLife 8:e42001 (2019).
J. Mitra, M. Makurath, T.T.M. Ngo, A. Troitskaia, Y.R. Chemla and T. Ha, “Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy”, PNAS 116, 8350-8359 (2019).
P. Kothari, V. Srivastava, V. Aggarwal, I. Tchernyshyov, J. Van Eyk, T. Ha and D. N. Robinson, “Contractility kits promote assembly of the mechanoresponsive cytoskeletal network”, J. Cell Sci. 132, jcs22670 (2019).
K. Dubiel, A. R. Myers, A. G. Kozlov, O. Yang, J. Zhang, T. Ha, T.M. Lohman and J.L. Keck, “Structural mechanisms of cooperative DNA binding by bacterial single-stranded DNA binding protein”, J. Mol. Biol. 431, 178-195 (2019).
M.H. Jo, W.T. Cottle and T. Ha, “Real-time measurement of molecular tension during cell adhesion and migration using multiplexed differential analysis of tension gauge tethers”, ACS Biomat. Sci. Eng. 5, 3856-3863 (2019).
Y. Ma and T. Ha, “Fight against background noise in stimulated emission depletion nanoscopy, Physical Biology 16:051002 (2019).
J. C. Lee, Y. Ma, K. Y. Han and T. Ha, “Accurate background subtraction in STED nanoscopy with polarization switching”, ACS Photonics 6, 1789-1797 (2019).
J. Mitra and T. Ha, “Nanomechanics and co-transcriptional folding of spinach and mango”, Nature Communications 10:4318 (2019).
I. Okafor, D. Singh, Y. Wang, M. Jung, H. Wang, J. Mallon, S. Bailey, J. K. Lee and T. Ha, “Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding” Nucleic Acids Research 47:11880 (2019).
J. Mitra and T. Ha, “Streamlining effects of extra telomeric repeat on telomere folding revealed by fluorescence-force spectroscopy”, Nucleic Acids Research 47:11044-11056 (2019).
2018
M. Figiel, M. Krepl, S. Park, J. Poznański, K. Skowronek, A. Gołąb, T. Ha, J. Šponer and M. Nowotnya, “Mechanism of polypurine tract primer generation by HIV-1 reverse transcriptase”, J. Biol. Chem. 293, 191-202 (2018).
W. Zhu, B.C. Kim, M. Wang, J. Huang, A. Isak, N. M. Bexiga, R. Monticone, T. Ha, E. G. Lakatta and S. S. An, “TGFb1 reinforces the mechanical phenotype of arterial aging in vascular smooth muscle cells through a long-range regulation of the cytoskeletal stiffness.” Scientific Reports 8:2668 (2018).
D. Singh and T. Ha, “Understanding the molecular mechanisms of the CRISPR toolbox using single molecule approaches”, ACS Chemical Biology 13, 516-526 (2018).
B. Hua, Y. Wang, S. Park, K.Y. Han, D. Singh, J.H. Kim, W. Cheng and T. Ha, “Single-molecule centroid localization algorithm improves the accuracy of fluorescence binding assays", Biochemistry 57, 1572-1576 (2018).
D. Singh, Y. Wang, J. Mallon, O. Yang, J. Fei, A. Poddar, D. Ceylan, S. Bailey and T. Ha, “Mechanisms of improved specificity of engineered Cas9s revealed by single molecule analysis”, Nature Structural & Molecular Biology 25, 347-354 (2018).
D. Singh, J. Mallon, A. Poddar, Y. Wang, R. Tippana, O. Yang, S. Bailey and T. Ha, “Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a)”, PNAS 115, 5444-5449 (2018).
F. Chowdhury, S. Doganay, B. J. Leslie, R. Singh, K. Amar, B. Talluri, S. Park, N. Wang and T. Ha, “Cdc42-dependent modulation of rigidity sensing and cell spreading in tumor repopulating cells”, Biochem. Biophys. Res. Commun 500, 557-563 (2018).
H. R. Koh, R. Roy, M. Sorokina, G.Q. Tang, D. Nandakumar, S. S. Patel and T. Ha, “Correlating transcription initiation and conformational changes by a single subunit RNA polymerase with near base pair resolution”, Mol. Cell 70, 695-706 (2018).
S. J. Lee, S. Syed and T. Ha, “Single-molecule FRET analysis of replicative helicases”, Methods in Molecular Biology, 1805, 233-250 (2018).
Hellenkamp et al, “Precision and accuracy of single-molecule FRET measurements - a worldwide benchmark study”, Nature Methods 15, 669-676 (2018).
X. Wang, S. Park, L. Zeng, A. Jain and T. Ha, “Towards single cell single-molecule pull-down”, Biophysical Journal 115, 283-288 (2018).
B. Huang, S. Panja, Y. Wang, S.A. Woodson and T. Ha, “Mimicking co-transcriptional RNA folding using a superhelicase”, J. Amer. Chem. Soc. 140, 10067-10070 (2018).
2017
I. Masuda, T. Igarasgi, R. Sakaguchi, R. Nitharwal, R. Takase, K.Y. Han, B. Leslie, C. Liu, H. Gamper Jr., T. Ha, S. Sanyal and Y.M. Hou, “A genetically encoded fluorescent tRNA is active in live-cell protein synthesis”, Nucleic Acids Research 45, 4081-4093 (2017).
V. C. Luca, B.C. Kim, C. Ge, S. Kakuda, D. Wu, M. Roein-Peikar, R. S. Haltiwanger, C. Zhu, T. Ha and K. C. Garcia, “Notch-Jagged complex structure implicates a catch bond in tuning ligand sensitivity”, Science 355, 1320-1324 (2017).
J. Xiao and T. Ha, “Flipping nanoscopy on its head”, Science 355, 582-584(2017).
T. Ha, “Growth factor rattled out of its cage”, Nature 542, 40-41 (2017).
C. T. Lin and T. Ha, “Probing single helicase dynamics on long nucleic acids through fluorescence-force measurements”, Methods in Molecular Biology, 1486, 295-316 (2017).
C. T. Lin, F. Tritschler, K. S. Lee, M. Gu, C. M. Rice and T. Ha, “Single-molecule imaging reveals the translocation and DNA looping dynamics of hepatitis C virus NS3 helicase”, Protein Science 26, 1391-1403 (2017).
I. T. S. Li, T. Ha and Y. R. Chemla, “Mapping cell surface adhesion by rotational tracking and adhesion footprinting”, Scientific Reports 7, 44502 (2017).
S. C. Abeysirigunawardena, H. Kim, J. Lai, K. Ragunathan, M. C. Rappe, Z. Luthey-Schulten, T. Ha and S. A. Woodson, “Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes”, Nature Comm., 8:492 (2017).
S. Panja, B. Hua, D. Zegarra, T. Ha and S. A. Woodson, “Transition folding in Mg2+ and transition metals activates Twister ribozyme”, Nature Chem. Biol. 13, 1109-1114 (2017).
C. T. Lin and T. Ha, “Visualization of helicase dynamics using fluorescence localization and optical trapping”, Methods in Enzymology, 582, 121-136 (2017).
P. Singh, S. K. Ramachandra, J, Zhu, B. C. Kim, D. Biswas, T. Ha, P. A. Iglesias and R. Li, “Sphingolipids facilitate age asymmetry of membrane proteins in dividing yeast cells”, Mol. Biol. Cell 18, 2712-2722 (2017).
S. Doganay, M. Y. Lee, A. Baum, J. Peh, S. Y. Hwang, J. Y. Yoo, P. J. Hergenrother, A. Garcia-Sastre, S. Myong and T. Ha, “Single-cell analysis of early antiviral gene expression reveals a determinant of stochastic IFNB1 expression”, Integrative Biology 9, 857-867 (2017).
J. Clatot, M. Hoshi, X. Wan, H. Liu, A. Jain, K. Shinlapawittayatorn, C. Marionneau, E. Ficker, T. Ha and I. Deschenes, “Voltage-Gated Sodium Channels Assemble and Gate as Dimers”, Nature Comm. 8:2077 (2017).
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 and T. Ha, “Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super-resolution”, Journal of Cell Science 130, 4180-4192 (2017).
2016
S. Wang, R. Vafabakhsh, W.F. Borschel, T. Ha and C.G. Nichols, “Structural dynamics of potassium channel gating revealed by single molecule FRET”, Nature Structural & Molecular Biology 23, 31-36 (2016).
T. Ngo, J. Yoo, Q. Dai, Q. Zhang, C. He, A. Aksimentiev and T. Ha, “Effect of Cytosine Modifications on DNA Flexibility and Nucleosome Mechanical Stability”, Nature Communications 7:10813 (2016).
J. Yoo, H. Kim, A. Aksimentiev and T. Ha, “Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation,” Nature Communications 7:11045 (2016).
T. Ha, “Probing nature’s nanomachines one molecule at a time”, Biophysical Journal 110, 1004-7 (2016).
M. Roein-Peikar, Q. Xu, X. Wang and T. Ha, “Ultrasensitivity of cell adhesion to the presence of mechanically strong ligands,” Physical Review X 6, 011001 (2016).
K. J. Molohon, P. M. Blair, S. Park, J. R. Doroghazi, T. Maxson, J. R. Hershfield, K. M. Flatt, N. E. Schroeder, T. Ha, and D. A. Mitchell, “Plantazolicin is an ultra-narrow spectrum antibiotic that targets Bacillus anthracis membrane,” ACS Infectious Disease 2, 207-220 (2016).
E. Arauz, V. Aggarwal, A. Jain, T. Ha and J. Chen, “Single-molecule analysis of lipid-protein interactions in crude cell lysates”, Analytical Chemistry 88; 4269-76 (2016).
X. Zong, S. Nakagawa, S. Freier, J. Fei, T. Ha, S. Prasanth and K. Prasanth, “Natural antisense RNA promotes 3’ end processing and maturation of MALAT1 lncRNA”, Nucleic Acids Research 44, 2898-908 (2016).
X. Wang, Z. Rahil, I.T.S. Li, F. Chowdhury, D.E. Leckband, Y.C. Chemla and T. Ha, “Constructing modular and universal single molecule tension sensor using protein G to study mechano-sensitive receptors”, Scientific Reports 6:21584 (2016).
M.D. Brenner, R. Zhou, D.E. Conway, L. Lanzano, E. Gratton, M.A. Schwartz and T. Ha, “Spider silk peptide is a compact, linear nano-spring ideal for intracellular tension sensing”, Nano Letters 16, 2096-2102 (2016).
M.K. Lee, J. Park, X. Wang, M. Roein-Peikar, E. Ko, E. Qin, J.H. Lee, T. Ha and H. Kong, “Rupture force of cell adhesion ligand tethers modulates biological activities of a cell-laden hydrogel”, Chemical Communications 52, 4757-60 (2016).
P. Heo, Y. Yang, K. Y. Han, B. Kong, J. H. Shin, Y. Jung, C. Jeong, J. Shin, Y. K. Shin, T. Ha and D. H. Kweon, “A chemical controller of SNARE-driven membrane fusion that primes vesicles for Ca2+-triggered millisecond exocytosis” J. Am. Chem. Soc. 138, 4512-21 (2016).
F. Chowdhury, I.T.S. Li, T.T.M. Ngo, B.J. Leslie, B.C. Kim, J.E. Sokoloski, E. Weiland, X. Wang, Y.R. Chemla, T.M. Lohman and T. Ha, “Defining single molecular forces required for Notch activation using nano yoyo”, Nano Letters 16, 3892-7 (2016).
A. Basu and T. Ha, “The light side of the force”, eLife, 5, e14274 (2016).
E. Nelson, K. Schmidt, L. Deflubé, S. Doğanay, L. Banadyga, J. Olejnik, A. Hume, E. Ryabchikova, H. Ebihara, N. Kedersha, T. Ha and E. Mühlberger, “Ebola virus does not induce stress granule formation during infection and sequesters stress granule proteins within viral inclusions”, J. Virology 90, 7268-84 (2016).
A. Husbands, V. Aggarwal, T. Ha and M. Timmermans, “In Planta Single-Molecule Pull-down (SiMPull) Reveals Tetrameric Stoichiometry of HD-ZIPIII: LITTLE ZIPPER Complexes”, Plant Cell 28, 1783-94 (2016).
Z. Rahil, S. Pedron, X. Wang, T. Ha, B. Harley and D. Leckband, “Nanoscale mechanics guides cellular decision making”, Integrative Biology, 8:929-35 (2016).
D. Singh, S. Sternberg, J. Fei, J. A. Doudna and T. Ha, “Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9”, Nature Communications 7, 12778 (2016).
V. Aggarwal and T. Ha, “Single-molecule fluorescence microscopy of native macromolecular complexes”, Curr. Opin. Struct. Biol. 41, 225-232 (2016).
2015
T. Ngo, Q. Zhang, R. Zhou, J. G. Yodh and T. Ha, “Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility”, Cell 160, 1135-1144 (2015).
S. H. Kim, J. Park, C. Joo, D. Kim and T. Ha, “Dynamic growth and shrinkage govern the pH dependence of RecA filament stability”, PLoS One 10:e0115611 (2015).
J. Fei, D. Singh, Q. Zhang, S. Park, D. Balasubramanian, I. Golding, C. K. Vanderpool and T. Ha, “Determination of in vivo target search kinetics of regulatory noncoding RNA”, Science 347, 1371-1374 (2015).
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 and Y. Wang, “Distinct mechanisms regulating mechanical force-induced Ca2+ signals at the plasma membrane and the endoplasmic reticulum in human mesenchymal stem cells”, eLife 4, e04876 (2015).
M. J. Comstock, K.D. Whitley, H. Jia, T.M. Lohman, T. Ha and Y. R. Chemla, “Direct observation of structure-function relationship in a nucleic acid processing enzyme”, Science 348, 352-354 (2015).
S. Arslan, R. Khafizov, C. D. Thomas, Y. R. Chemla and T. Ha, “Engineering of a superhelicase through conformational control”, Science 348, 344-347 (2015).
T. Ngo and T. Ha, “Nucleosomes undergo slow spontaneous gaping”, Nucleic Acids Research 43, 3964-3971 (2015).
S. Giri, V. Aggarwal, J. Pontis, Z. Shen, A. Chakraborty, A. Khan, C. Mizzen, K. Prasanth, S. Ait-Si-Ali, T. Ha and S. Prasanth, “The preRC protein ORCA Organizes Heterochromatin by Assembling Histone H3 Lysine 9 Methyltransferases on Chromatin”, eLife 4, e06496 (2015).
K. Y. Han and T. Ha, “Dual-color three-dimensional STED microscopy with a single high-repetition-rate laser”, Optics Letters 40, 2653-2656 (2015).
A. Khan, S. Giri, Y. Wang, A. Chakraborty, A. K. Ghosh, A. Anantharaman, V. Aggarwal, K. M. Sathyan, T. Ha, K. V. Prasanth and S. G. Prasanth, “BEND3 represses rDNA transcription by stabilizing a NoRC component via UPS21 deubiquitinase”, PNAS 112, 8338-8343 (2015).
D. Sewell, H. Kim, T. Ha and P. Ma, “A parameter estimation method for fluorescence lifetime data,” BMC Res Notes 9;8, 230 (2015)
F. Chowdhury, I.T.S. Li, B. J. Leslie, S. Doganay, R. Singh, X. Wang, J. Seong, S.H. Lee, S. Park, N. Wang and T. Ha, “Single molecular force across single integrins dictates cell spreading”, Integrative Biology 7, 1265-1271 (2015).
N. Shashikanth, Y. I. Petrova, S. Park, J. Chekan, S. Maiden, M. Spano, T. Ha, B. M. Gumbiner and D. E. Leckband, “Allosteric regulation of E-cadherin adhesion”, J. Biol. Chem. 290, 21749-21761 (2015).
H. R. Lee, J. Mitra, S. J. Gao, T. K. Oh, M. Kim, T. Ha and J. U. Jung, “KSHV vIRF4 perturbs the G1-S cell cycle progression via deregulation of cyclin D1”, J. Virology 90, 1139-43 (2015).
J. R. Peterson, J. A. Cole, J. Fei, T. Ha and Z. Luthey-Schulten, “Effect of DNA replication on transcriptional noise”, PNAS 112, 15886-15891 (2015).
J. Zhang, J. Fei, B. J. Leslie, K. Y. Han, T. E. Kuhlman and T. Ha, “Tandem “Spinach” Array for mRNA Imaging in Living Bacterial Cells”, Scientific Reports 5:17295 (2015).
X. Wang, J. Sun, Q. Xu, F. Chowdhury, M. Roein-Peikar, Y. Wang and T. Ha, “Integrin molecular tension within motile focal adhesions”, Biophysical Journal 109, 2259-2267 (2015).
2014
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, and J. U. Jung, “Crosstalk between the cGAS DNA Sensor and Beclin-1 Autophagy Protein Shapes Innate Antimicrobial Immune Responses”, Cell Host & Microbe 15:2, 228-238 (2014).
G.-Q. Tang, D. Nandakumar, R. P. Bandwar1, K. S. Lee, R. Roy, T. Ha and S. S. Patel, “Relaxed rotational and scrunching changes in P266L mutant of T7 RNA polymerase reduces short abortive RNAs while delaying transition into elongation”, PLoS One 9:e91859 (2014).
S. Syed, M. Pandey, S. S. Patel, and T. Ha, “Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase”, Cell Reports 6, 1–9 (2014).
B. Bhattacharyya, N. P. George, T. M. Thurmes, R. Zhou, N. Jani, S. R. Wessel, S. J. Sandler, T. Ha and J. L. Keck, “Structural mechanisms of PriA-mediated DNA replication restart”, PNAS 111:, 1373-1378 (2014).
J. Zhang, R. Zhou, J. Inoue, T. Mikawa and T. Ha, “Single molecule analysis of Thermus thermophiles SSB protein dynamics on single-stranded DNA”, Nucleic Acids Research 42, 3821-32 (2014).
H. Lee, S. Doganay, B. Chung, Z. Toth, K. Brulois, S. Lee, Z. Kanketanyeva, P. Feng, T. Ha, and J. U. Jung, “Kaposi's sarcoma-associated herpesvirus viral interferon regulatory factor 4 (vIRF4) targets expression of cellular IRF4 and the Myc gene to facilitate lytic replication”, J. Virology, 88, 2183-94 (2014).
H. Kim, S. C. Abeysirigunawardena, K. Chen, M. Mayerle, K. Ragunathan, Z. Luthey-Schulten, T. Ha and S. A. Woodson, “Protein-guided RNA dynamics during early ribosome assembly”, Nature 506, 334-8 (2014).
S. J. Lee, S. Syed , E. J. Enemark , S. Schuck , A. Stenlund , T. Ha and L. Joshua-Tor, “A dynamic look at DNA unwinding by a replicative helicase”, Proc. Natl. Acad. Sci. USA, 111, E827-35 (2014).
J. Peterson, P. Labhsetwar, J. R. Ellermeier, P.R.A. Kohler, A. Jain, T. Ha, W. W. Metcalf, and Z. A. Luthey-Schulten, "Towards a computational model of a methane producing archaeum”, Archaea 2014:898453 (2014).
R. Zhou, J. Zhang, M. L. Bockman, V. A. Zakian and T. Ha, “Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA”, eLife 3:e02190 (2014).
K. S. Lee, A. B. Marciel, A. G. Kozlov, C. M. Schroeder, T. M. Lohman and T. Ha, “Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer”, J. Mol. Bio., 426, 2413-21 (2014).
C. Maffeo, T. Ngo, T. Ha, A. Aksimentiev, “A coarse-grained model of unstretched single-stranded DNA derived from atomistic simulation and single-molecule experiment”, J. Chem. Theory Comput 10, 2891–2896 (2014).
Y. Tan, A. Tajik, J. Chen, Q. Jia, F. Chowdhury, L. Wang, J. Chen, S. Zhang, Y. Hong, H. Yi, D. Wu, Y. Zhang, F Wei, Y.-C. Poh, R. Singh, J. Seong, L.-J. Lin, S. Doğanay, Y. Li, H. Jia, T. Ha, Y. Wang, B. Huang and N. Wang, "Matrix softness regulates plasticity of tumor-repopulating cells via H3K9 demethylation and Sox2 expression”, Nature Communications 5:4619, doi:10.1038/ncomms5619 (2014).
K. Kondabagil, L. Dai, R. Vafabakhsh, T. Ha, B. Draper and V. Rao, “Designing a nine cysteine-less DNA packaging motor from bacteriophage T4 reveals new insights into ATPase structure and function”, Virology, 468-470, 660-668 (2014).
R. Vafabakhsh, K. Kondabagil, T. Earnest, K. Lee, Z. Zhang, L. Dai, K. A. Dahmen, V. B. Rao and T. Ha, “Single molecule packaging initiation in real-time by a viral DNA packaging machine from bacteriophage T4”, Proc. Natl. Acad. Sci. USA 111, 15096-15101 (2014).
S. Müller, K. Laxmi-Reddy, P. V. Jena, B. Baptiste, Z. Dong, F. Godde, T. Ha, R. Rodrguez, S. Balasubramanian and I. Huc, “Targeting DNA G-Quadruplexes with Helical Small Molecules”, ChemBioChem 15, 2563-2570 (2014).
T. Ha, “Single Molecule Methods Leap Ahead”, Nature Methods 11, 1015-1018 (2014).
B. Hua, K.Y. Han, R. Zhou, H. Kim, X. Shi, S. C. Abeysirigunawardena, A. Jain, D. Singh, V. Aggarwal, S. A. Woodson and T. Ha, “An improved single molecule passivation method for single molecule studies”, Nature Methods 11, 1233-1236 (2014).
S. H. Kim, K. Ragunathan, J. Park, C. Joo, D. Kim and T. Ha, “Cooperative conformational transitions keep RecA filament active during ATPase cycle”, J. Am. Chem. Soc. 136:42, 14796-14800 (2014).
V. Aggarwal and T. Ha, “Single-molecule pull-down (SiMPull) for new-age biochemistry”, Bioessay, doi: 10.1002/bies.201400090 (2014).
A. Jain, E. Arauz, V. Aggarwal, N. Ikon, J. Chen and T. Ha, “Stoichiometry and assembly of mTOR complexes revealed by single-molecule pull-down”, Proc. Natl. Acad. Sci. USA 111, 17833-17838 (2014).
C. J. Thibodeaux, T. Ha and W. A. van der Donk, “A price to pay for relaxed substrate specificity: A comparative kinetic analysis of the class II lanthipeptide synthetases, ProcM and HalM2”, J. Am. Chem. Soc. 136:50, 17513-17529 (2014).
2013
S. H. Yang, R. Zhou, J. Campbell, J. Chen, T. Ha and T.T. Paull, “The SOSS1 single-stranded DNA binding complex promotes DNA end resection in concert with Exo1”, EMBO J. 32, 126-139 (2013).
D. N. Ermolenko, P. V. Cornish, T. Ha and H. F. Noller, “Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation”, RNA 19, 158-166 (2013).
N. F. Lue, R. Zhou, L. Chico, N. Mao, O. Steinberg-Neifach and T. Ha, “The telomere capping complex CST has an unusual stoichiometry, makes multipartite interaction with G-tails, and unfolds higher-order G-tail structures”, PLoS Genetics 9, e1003145 (2013).
H. Kim and T. Ha, “Single molecule nanometry for biological physics”, Reports on Progress in Physics 76, 016601 (2013).
Y. Lai, J. Diao, Y. Liu, Y. Ishitsuka, Z. Su, K. Schulten, T. Ha and Y.K. Shin, “Fusion pore formation and expansion induced by Ca2+ and synaptotagmin 1”, PNAS 110, 1333-1338 (2013).
X. Wang and T. Ha, “Defining Single Molecular Forces Required to Activate Integrin and Notch Signaling”, Science 340, 991-994 (2013).
K. S. Lee, H. Balci, H. Jia, T. M. Lohman and T. Ha, “Direct imaging of single UvrD helicase dynamics on long single-stranded DNA”, Nature Commun. 4, 1878 (2013).
J. A. Lamboy, H. Kim, H. Dembinski, T. Ha and E. A. Komives, “Single molecule FRET reveals the native state dynamic of the IκBα ankyrin repeat domain”, J. Mol. Biol. 425, 2578-2590 (2013).
S. K. Yang, X. Shi, S. Park, T. Ha, S. C. Zimmerman, “A dendritic single-molecule fluorescent probe that is monovalent, photostable, and minimally blinking”, Nature Chem. 5, 692-697 (2013).
S. R. Wessel, A. H. Marceau, S. C. Massoni, R. Zhou, T. Ha, S. J. Sandler and J. L. Keck, "PriC-mediated DNA replication restart requires PriC complex formation with the single-stranded DNA-binding protein”, J. Biol. Chem. 288, 17569-17578 (2013).
S. H. Kim, C. Joo, T. Ha and D. Kim, “Molecular mechanism of sequence-dependent stability of RecA filament”, Nucleic Acids Research 41, 7738-7744 (2013).
J. Patel, A. Jain, Y.Y. Chou, A. Baum, T. Ha and A. Garcia-Sastre, “ATPase-driven oligomerization of RIG-I on RNA allows optimal activation of type-I interferon”, EMBO Reports 14, 780-787 (2013).
T. Ha, “Single molecule approaches embrace molecular cohorts”, Cell 154, 723-726 (2013).
K. Y. Han, B. Leslie, J. Fei, J. Zhang, and T. Ha, “Understanding the photophysics of the Spinach-DFHBI RNA aptamer-fluorogen complex to improve live cell RNA imaging”, J. Am. Chem. Soc 135, 19033-19038 (2013).
J. Fei and T. Ha, "Watching DNA breath one molecule at a time”, Proc. Natl. Acad. Sci. USA, 110, 17173-17174 (2013).
2012
E. A. Morrison, G. T. DeKoster, S. Dutta, R. Vafabakhsh, M. Charkson, A. Bahl, D. Kern, T. Ha and K. A. Henzler-Wildman, “Antiparallel EmrE exports drugs by exchanging between asymmetric structures”, Nature 481, 45-50 (2012).
T. Ha and P. Tinnefeld, “Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging”, Annual Review of Physical Chemistry 63, 595-617 (2012).
T. Ha, A. G. Kozlov and T. M. Lohman, "Single-molecule views of protein movement on single-stranded DNA”, Annual Review of Biophysics 41, 295-319 (2012).
A. Jain, R. Liu, Y.K. Xiang and T. Ha, “Single-molecule pull-down for studying protein interactions”, Nature Protocols 7, 445–452 (2012).
X. Shi, Y. Jung, L.J. Lin, C. Liu, C. Wu, I.K.O. Cann and T. Ha, “Quantitative fluorescence labeling of aldehyde-tagged proteins for single-molecule imaging”, Nature Methods 9, 499-503 (2012).
J. Diao, Y. Ishitsuka, H.K. Lee, C. Joo, Z. Su, S. Syed, Y.K. Shin, T.Y. Yoon and T. Ha, “A single vesicle-vesicle fusion assay for in vitro studies of SNAREs and accessory proteins”, Nature Protocols 7, 912-934 (2012).
K. Chen, J. Eargle, J. Lai, H. Kim, S. Abeysirigunawardena, M. Mayerle, S.A. Woodson, T. Ha and Z. Luthey-Schulten, "Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Go simulations”, J. Phys. Chem. B 116, 6819-6831(2012).
Q. Gao, Y.Y. Chou, S. Doganay, R. Vafabakhsh, T. Ha and P. Palese, “The influenza A virus PB2, PA, NP and M segments play a pivotal role during genome packaging”, J. Virology 86, 7043-51 (2012).
Y.Y. Chou, R. Vafabakhsh, S. Doğanay, Q. Gao, T. Ha and P. Palese, “One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis”, PNAS, 109, 9101-9106 (2012).
I. Cisse, H. Kim and T. Ha, “A rule of seven in Watson-Crick base pairing of mismatched sequences”, Nature Structural & Molecular Biology 19, 623-627 (2012).
G. Lee and T. Ha, “Single-molecule imaging: A collagenase pauses before embarking on a killing spree”, Current Biology 22 (12), R499–R501 (2012).
Z. Shen, A. Chakraborty, A. Jain, S. Giri, T. Ha, K. V. Prasanth and S. G. Prasanth, “Dynamic association of ORCA with pre-RC components regulates DNA replication initiation”, Mol. Cell. Biol. 32, 3107-20 (2012).
G. Lee, M. Bratkowski, F. Ding, A. Ke and T. Ha, “Elastic coupling between RNA degradation and unwinding by an exoribonuclease”, Science, 336, 1726-1729 (2012).
R. Vafabakhsh and T. Ha, “Extreme bendability of DNA less than 100 base pairs long revealed by single molecule cyclization”, Science 337, 1097-1101 (2012).
M.S. Panter, A. Jain, R.M. Leonhardt, T. Ha and P. Cresswell, “Dynamics of major histocompatibility complex class I association with the human peptide-loading complex”, J. Biol. Chem. 287, 31172–31184 (2012).
R. Zhou and T. Ha, “Single-molecule analysis of SSB dynamics on single-stranded DNA”, Methods Mol. Biol. 922, 85-100 (2012).
M. Schlierf and T. Ha, “A helicase with an extra spring in its step”, Cell 151, 244-246 (2012).
K. Ragunathan, C. Liu and T. Ha, “RecA filament sliding on DNA facilitates homology search”, eLife 1, e00067 (2012).
K. Shen, S. Arslan, D. Akopian, T. Ha and S. Shan, “Activated GTPase movement on an RNA scaffold drives cotranslational protein targeting”, Nature 492, 271-275 (2012).