Publications

Fluorescence lifetime analysis of smFRET with contribution of PIFE on donor and acceptor | bioRxiv 

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

Single molecule FRET analysis of CRISPR Cas9 single guide RNA folding dynamics

Okafor and T. Ha

 Journal of Physical Chemistry B 127, 45-51(2023) (📄 pdf).

Senescent stroma induces nuclear deformations in cancer cells via the inhibition of RhoA/ROCK/myosin II-based cytoskeletal tension

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,

 PNAS Nexus, 2, pgac270 (2023) (📄 pdf).

Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins

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

Nature Methods 20, 523-535 (2023) (📄 pdf).

Biallelic TTI1 variants cause an autosomal recessive neurodevelopmental disorder with microcephaly

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

 American Journal of Human Genetics 110, 499-515 (2023) (📄 pdf).

Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq+

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 

Nature Methods 20, 706-713 (2023) (📄 pdf).

Sniper2L, a high-fidelity Cas9 variant with high activity

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

Nature Chemical Biology 19, 972-980 (2023) (📄 pdf).

The START domain potentiates HD-ZIPIII transcriptional activity

A. Husbands, A. Feller, V. Aggarwal, C. E. Dresden, A. S. Holub, T. Ha and M.C.P. Timmermans

Plant Cell 35, 2332-2348 (2023) (📄 pdf).

DNA damage-induced S-phase specific phosphorylation of Orc6 is critical for the maintenance of genome stability

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 

Molecular and Cellular Biology 43, 143-156 (2023) (📄 pdf).

Dimensional Reduction for Single Molecule Imaging of DNA and Nucleosome Condensation by polyamines, HP1 and Ki-67

N. Benning, J. Kaeligstel-Hansen, F. Rashid, S. Park, R. Merino Urteaga, T.W. Liao, J. Hao, J. M. Berger, N. Hatzakis & T. Ha 

Journal of Physical Chemistry B 127, 1922-1931 (2023) (📄 pdf).

Membrane compression by synaptic vesicle exocytosis triggers ultrafast endocytosis

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

Nature Communications 14:2888 (2023) (📄 pdf).

Bursting translation on single mRNA in live cells

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 

Molecular Cell 83, 2276-2289 (2023) (📄 pdf).

Mapping the dynamics of DNA repair with emerging CRISPR technologies

Y. Liu, W.T. Cottle and T. Ha

Trends in Genetics 39, P560-574 (2023) (📄 pdf). 

Linking folding dynamics and function of SAM/SAH riboswitch at the single molecule level

T.-W. Liao, L. Huang, T.J. Wilson, L. Ganser, D.M.J. Lilley and T. Ha

 Nucleic Acids Research 51, 8957-8969 (2023) (📄 pdf).

Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice

R. A. Deshpande, A. Marin-Gonzalez, H. K. Barnes, P. R. Woolley, T. Ha and T. T. Paull 

Nature Communications 14:5759 (2023) (📄 pdf).

Mind your tag in single molecule measurements

R. Merino-Urteaga and T. Ha 

Cell Reports Methods 3:100623 (2023) (📄 pdf).

Direct uphill strand displacement with an engineered super-helicase

H. Hall-Thomsen, S. Small, M. Gavrilov, T. Ha, R. Schulman and P. Moerman 

ACS Synthetic Biology 12, 3424-3432 (2023) (📄 pdf).

Enhanced mTORC1 signaling and protein synthesis in pathologic α-synuclein cellular and animal models of Parkinson’s disease

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 

Science Translational Medicine 15, eadd0499 (2023) (📄 pdf).

Helicase activity modulation with on-demand light-based conformational control

D. Bobrovnikov, M. Makurath, C. H. Wolfe, Y. R. Chemla and T. Ha

J. Amer. Chem. Soc. 145, 21253-21262 (2023) (📄 pdf).

SIKs regulate HDAC7 stabilization and cytokine recall in late-stage T -cell effector differentiation

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 

J. Immunology 122, 1767-1782 (2023) (📄 pdf).

Membrane Ruffling is a Mechanosensor of Extracellular Fluid Viscosity

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 

Nature Physics 18, 1112–1121 (2022) (📄 pdf).

Next Generation Single Molecule Techniques: Imaging, Labeling and Manipulation in vitro and in cellulo

T. Ha, C. Kaiser, S. Myong, B. Wu and J. Xiao, 

Molecular Cell 82, 304-314 (2022) (📄 pdf).

Coordinated DNA and Histone Dynamics Drive Accurate Histone H2A.Z Exchange

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

Science Advances 8, eabj5509 (2022) (📄 pdf).

Improving the specificity of nucleic acid detection with endonuclease-actuated degradation

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 

Communications Biology 5:290 (2022) (📄 pdf).

Sequence-dependent mechanochemical coupling of helicase translocation and unwinding at single-nucleotide resolution

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 

PNAS 119, e2202489119 (2022).

Catalytic DNA polymerization can be expedited by active product release

P. Moerman, M. Gavrilov, T. Ha and R. Schulman, Angewandte 

Chemie e202114581 (2022).

Rtt105 regulates RNA function by configurationally stapling the flexible domains

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 

Nature Communications 13:5152 (2022).

ATP binding facilitates target search SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA

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 

eLife 11, e77352 (2022).

Vectorial folding of telomere overhangs promotes higher accessibility

T. Paul, P. L. Opresko, T. Ha and S. Myong 

Nucleic Acids Research 50, 6271-6283 (2022).

Orc6 is a component of the replication fork and enables efficient mismatch repair

Y.C. Lin, A. Chakraborty, J. Mitra, R. Hsu, M. K. Arif, S. Adusumilli, T. Ha, K. Prasanth, and S. Prasanth 

PNAS 119, e2121406119 (2022).

Dynamic condensates are primed at endocytic sites for ultrafast endocytosis

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 

Neuron 110, 2815-2835 (2022).

Engineering functional membrane-membrane interface by InterSpy

H. Moghimianavval, C. Patel, S. Mohapatra, S.W. Hwang, T. Kayikcioglu, Y. Bashirzadeh, A.P. Liu and T. Ha, 

Small  26:e2202104 (2022).

AAA+ ATPase Thorase inhibits mTOR signaling through the disassembly of the mTOR complex 1

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 

 Nature Communications 13:4836 (2022).

β2-integrin adhesive bond tension under shear stress modulates cytosolic calcium flux and neutrophil inflammatory response

V. A. Morikis, J. Madigan, M. H. Jo, S. J. Chen, L. C. Werba, T. Ha, S. I. Simon 

Cells 11, 1822 (2022). 

Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites

R. S. Zou, A. Marin-Gonzalez, Y. Liu, H. B. Liu, L. Shen, R. Dveirin, J.X.J. Luo, R. Kalhor and T. Ha

Nature Cell Biology 24, 1433-1444 (2022).

Engineered helicase eliminates thermocycler from DNA amplification while retaining desired PCR characteristics

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, 

Nature Communications 13:6312 (2022).

Single molecule characterization of subtype-specific β1 integrin mechanics

M.H. Jo, J. Li, V. Jaumouille, Y. Hao, J. Coppola, J. Yan, C.M. Waterman, T.A. Springer and T. Ha

 Nature Communications 13:1471 (2022)

Deciphering the mechanical code of the genome and epigenome

A. Basu, D. Bobrovnikov, B. Cieza, J. P. Arcon, Z. Qureshi, M. Orozco and T. Ha 

Nature Struct. Mol. Bio. 29, 1178-1187 (2022).

Achieving single nucleotide sensitivity in direct hybridization genome imaging

Y. Wang. W. T. Cottle, H. Wang, M. Gavrilov, R. S. Zou, M-T. Pham, S. Yegnasubramanian, S. Bailey and T. Ha, 

Nature Communications, 13, 7776 (2022).

Measuring DNA mechanics on the genome scale

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

 Nature 589, 462-467 (2021). 

Cas9 deactivation with photocleavable guide RNAs

R. S. Zou, Y. Liu, B. Wu and T. Ha 

Molecular Cell 81:1553-1565 (2021).

COL2A1 is a novel biomarker of melanoma tumor repopulating cells

B. Talluri, K. Aamr, M. Saul, T. Shireen, V. Konjufca, J. Ma, T. Ha and F. Chowdhury 

Biomedicine 8, 360 (2020).

Crystal structure and ligand-induced folding of the SAM/SAH riboswitch

L. Huang, T.W. Liao, J. Wang, T. Ha, and D.M.J. Lilley 

Nucleic Acids Research 48, 7545-7556 (2020)

Real-time monitoring of single ZTP riboswitches reveals a complex and kinetically controlled decision landscape

B. Hua, C. P. Jones, J. Mitra, P. J. Murray, R. Rosenthal, A. R. Ferre-D’Amare and T. Ha 

 Nature Communications 11, 4531 (2020).

Increasing proximity promotes MST2 autophosphorylation during Hippo signaling

T. Tran, J. Mitra, T. Ha and J.M. Kavran 

J Biol Chem 295, 16166-16179 (2020).

Stochastic analysis probes the role of the chaperone Hfq in E. coli sugar shock response

D.M. Bianchi, T.A. Brier, A. Poddar, M.S. Azam, C.K. Vanderpool, T. Ha and Z. Luthey-Schulten 

Frontiers in Molecular Biosciences 7:593826 (2020).

Mechanical stress determines the configuration of TGFβ activation in articular cartilage

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 

Nature Communications 12:1706 (2021).

Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA

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

 Nature Communications, 12:874 (2021).

Real-time observation of Cas9 post-catalytic domain motions

Y. Wang, J. Mallon, H. Wang, D. Singh, M. H. Jo, B. Hua, S. Bailey and T. Ha 

PNAS 118:e2010650118 (2021).

Genome Oligopaint via Local Denaturing Fluorescence In situ Hybridization

Y. Wang, W.T. Cottle, H. Wang, X.A. Feng, J. Mallon, M. Gavrilov, S. Bailey and T. Ha 

Molecular Cell 81:1566-1577 (2021).

DNA Sequence and Methylation Prescribe the Inside-Out Conformational Dynamics and Bending Energetics of DNA Minicircles

J. Yoo, S. Park, C. Maffeo, T. Ha and A. Aksimentiev 

Nucleic Acids Research 49:11459-11475 (2021)

Hippocampal AMPA receptor-auxiliary subunit structures and mechanism of allosteric inhibition

J. Yu, P. Rao, S. Clark, J. Mitra, T. Ha and E. Gouaux 

Nature 594, 448-453 (2021)

DNA mechanics and its impact on biological processes

A. Basu and T. Ha 

J. Mol. Biol. 433:166861 (2021).

Molecular nanomechanical mapping of histamine-induced smooth muscle cell contraction and shortening

M.H. Jo, B.C. Kim, K. Sung, R.A. Panettieri, S.S. An, J. Liu and T. Ha 

ACS Nano 15, 11585–11596 (2021).

Multiple color single molecule FRET for DNA and RNA processes

X. A. Feng, M. F. Poyton and T. Ha 

Current Opinion in Structural Biology 70, 26-33 (2021). 

Regeneration of PEG slide for multiple rounds of single-molecule measurements

T. Paul, T. Ha and S. Myong  

Biophysical Journal 120, 1788-1799 (2021) 

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

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 

eLife, 10:e60416 (2021).

A viral genome packaging ring-ATPase is a flexibly coordinated pentamer

L. Dai, D. Singh, S. Lu, V. Kottadiel, R. Vafabakhsh, M. Mahalingam, Y.R. Chemla, T. Ha and V. Rao 

Nature Communications 12:6546 (2021) 

Redefining the specificity of phosphoinositide-binding by human PH domain-containing proteins

N. Singh, A. Reyes-Ordonez, M.A. Compagnone, J.F. Moreno-Castillo, B.J. Leslie, T. Ha and J. Chen 

Nature Communications 12:4339 (2021).

Single molecule analysis and engineering of DNA motors

S. Mohapatra, C. T. Lin, X. A. Feng, A. Basu and T. Ha 

Chemical Reviews 120, 36-78, (2020)

Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS

M. Bobrovskyy, J. Frandsen, J. Zhang, A. Poddar, M. S. Azam, T. M. Henkin, T. Ha and C. K. Vanderpool 

Molecular Microbiology 112, 1198-1218 (2019)

Very fast CRISPR on demand

Y. Liu, R. S. Zou, S. He, Y. Nihongaki, X. Li, S. Razavi, B. Wu and T. Ha 

Science 368, 1265–1269 (2020)

Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases

N. Su, A. K. Byrd, S. R. Bharath, O. Yang, Y. Jia, X. Tang, T. Ha, K. D. Raney and H. Song 

Nature Communications 10:5375 (2019)

Light-controlled twister ribozyme with single molecule detection resolves RNA function in time and space

A. Korman, H. Sun, B. Hua, H. Yang, J. N. Capilato, R. Paul, S. Panja, T. Ha, M. M. Greenberg and S.A. Woodson 

PNAS, 117, 12080-12086 (2020)

Just Took a DNA Test, Turns Out 100% Not That Phase

A.D. Gitler, J. Shorter, T. Ha and S. Myong 

Molecular Cell, 78, 193-194 (2020)

ORCA/LRWD1 regulates homologous recombination at ALT-telomeres by modulating heterochromatin organization

R. Hsu, Y. C. Lin, D. Singh, Y. Wang, V. Aggarwal, J. Mitra, A. Matur, T. Ha, K. Prasanth and S. Prasanth

 iScience 23, 101038 (2020)

Force-Dependent Trans-endocytosis by Breast Cancer Cells Depletes Costimulatory Receptor CD80 and Attenuates T Cell Activation

S. Park. Y. Shi, B.C. Kim, M.H. Jo, L. Cruz, Z. Gou, T. Ha, L.F. Lu, D. Reich and Y. Chen 

Biosensors and Bioelectronics 165, 112389 (2020) 

E. coli Rep helicase and RecA recombinase unwind G4 DNA and are important for resistance to G4-stabilizing ligands

T. Paul, A. Voter, R. Cuny, M. Gavrilov, T. Ha, J. Keck and S. Myong 

Nucleic Acids Research 48, 6640-6653 (2020)

ALS/FTLD-linked mutations in FUS glycine residues cause accelerated gelation and reduced interactions with wild-type FUS

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 

Molecular Cell 80, 666-681 (2020)

Conformational heterogeneity allows access to DNA in longer transcription activator-like effect (TALE) arrays

K. Geiger-Schuller, J. Mitra, T. Ha and D. Barrick 

eLife 8:e38298 (2019)

Measuring molecular mass with light

K.Y. Han and T. Ha

 Nature Photonics 12, 380-381 (2018)

Nuclear speckle fusion via long-range directional motion regulates the number and size of speckles

J. Kim, N. Khana, K. Y. Han, T. Ha and A. S. Belmont 

J. Cell Sci. 132: jcs226563 (2019)

Junction resolving enzymes use multivalent interaction to keep the Holliday junction dynamic

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 

Nat. Chem. Biol. 15, 269-275 (2019)

Hexameric helicase G40P unwinds DNA in single base pair steps

M. Schlierf, G. Wang, X. S. Chen and T. Ha 

eLife 8:e42001 (2019)

Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy

J. Mitra, M. Makurath, T.T.M. Ngo, A. Troitskaia, Y.R. Chemla and T. Ha 

PNAS 116, 8350-8359 (2019)

Contractility kits promote assembly of the mechanoresponsive cytoskeletal network

P. Kothari, V. Srivastava, V. Aggarwal, I. Tchernyshyov, J. Van Eyk, T. Ha and D. N. Robinson 

J. Cell Sci. 132, jcs22670 (2019)

Structural mechanisms of cooperative DNA binding by bacterial single-stranded DNA binding protein

K. Dubiel, A. R. Myers, A. G. Kozlov, O. Yang, J. Zhang, T. Ha, T.M. Lohman and J.L. Keck

 J. Mol. Biol. 431, 178-195 (2019)

Real-time measurement of molecular tension during cell adhesion and migration using multiplexed differential analysis of tension gauge tethers

M.H. Jo, W.T. Cottle and T. Ha 

ACS Biomat. Sci. Eng. 5, 3856-3863 (2019)

Fight against background noise in stimulated emission depletion nanoscopy

Y. Ma and T. Ha 

Physical Biology 16:051002 (2019)

Accurate background subtraction in STED nanoscopy with polarization switching

J. C. Lee, Y. Ma, K. Y. Han and T. Ha 

ACS Photonics 6, 1789-1797 (2019)

Nanomechanics and co-transcriptional folding of spinach and mango

J. Mitra and T. Ha 

Nature Communications 10:4318 (2019)

Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding

I. Okafor, D. Singh, Y. Wang, M. Jung, H. Wang, J. Mallon, S. Bailey, J. K. Lee and T. Ha

Nucleic Acids Research 47:11880 (2019)

Streamlining effects of extra telomeric repeat on telomere folding revealed by fluorescence-force spectroscopy

J. Mitra and T. Ha 

Nucleic Acids Research 47:11044-11056 (2019)

Mechanism of polypurine tract primer generation by HIV-1 reverse transcriptase

M. Figiel, M. Krepl, S. Park, J. Poznański, K. Skowronek, A. Gołąb, T. Ha, J. Šponer and M. Nowotnya 

J. Biol. Chem. 293, 191-202 (2018)

TGFb1 reinforces the mechanical phenotype of arterial aging in vascular smooth muscle cells through a long-range regulation of the cytoskeletal stiffness

W. Zhu, B.C. Kim, M. Wang, J. Huang, A. Isak, N. M. Bexiga, R. Monticone, T. Ha, E. G. Lakatta and S. S. An 

Scientific Reports 8:2668 (2018)

Understanding the molecular mechanisms of the CRISPR toolbox using single molecule approaches

D. Singh and T. Ha 

ACS Chemical Biology 13, 516-526 (2018)

Single-molecule centroid localization algorithm improves the accuracy of fluorescence binding assays

B. Hua, Y. Wang, S. Park, K.Y. Han, D. Singh, J.H. Kim, W. Cheng and T. Ha 

Biochemistry 57, 1572-1576 (2018)

Mechanisms of improved specificity of engineered Cas9s revealed by single molecule analysis

D. Singh, Y. Wang, J. Mallon, O. Yang, J. Fei, A. Poddar, D. Ceylan, S. Bailey and T. Ha 

 Nature Structural & Molecular Biology 25, 347-354 (2018)

Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a)

D. Singh, J. Mallon, A. Poddar, Y. Wang, R. Tippana, O. Yang, S. Bailey and T. Ha 

 PNAS 115, 5444-5449 (2018)

Cdc42-dependent modulation of rigidity sensing and cell spreading in tumor repopulating cells

F. Chowdhury, S. Doganay, B. J. Leslie, R. Singh, K. Amar, B. Talluri, S. Park, N. Wang and T. Ha 

Biochem. Biophys. Res. Commun 500, 557-563 (2018)

Correlating transcription initiation and conformational changes by a single subunit RNA polymerase with near base pair resolution

H. R. Koh, R. Roy, M. Sorokina, G.Q. Tang, D. Nandakumar, S. S. Patel and T. Ha 

Mol. Cell 70, 695-706 (2018)

Single-molecule FRET analysis of replicative helicases

S. J. Lee, S. Syed and T. Ha 

Methods in Molecular Biology, 1805, 233-250 (2018)

Precision and accuracy of single-molecule FRET measurements - a worldwide benchmark study

Hellenkamp et al 

Nature Methods 15, 669-676 (2018)

Towards single cell single-molecule pull-down

X. Wang, S. Park, L. Zeng, A. Jain and T. Ha 

Biophysical Journal 115, 283-288 (2018)

Mimicking co-transcriptional RNA folding using a superhelicase

B. Huang, S. Panja, Y. Wang, S.A. Woodson and T. Ha 

J. Amer. Chem. Soc. 140, 10067-10070 (2018)

1. 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).

2. 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).

3. J. Xiao and T. Ha, “Flipping nanoscopy on its head”, Science 355, 582-584(2017).

4. T. Ha, “Growth factor rattled out of its cage”, Nature 542, 40-41 (2017).

5. 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).

6. 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).

7. 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).

8. 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).

9. 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).

10. C. T. Lin and T. Ha, “Visualization of helicase dynamics using fluorescence localization and optical trapping”, Methods in Enzymology, 582, 121-136 (2017).

11. 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).

12. 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).

13. 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).

14. 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).

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).