Cohesin drives chromatin scanning during the RAD51-mediated homology search.

Marin-Gonzalez A, Rybczynski AT, Nilavar NM, Nguyen D, Karwacki-Neisius V, Li AG, Zou RS, Avilés-Vázquez FJ, Kanemaki MT, Scully R, Ha T.

bioRxiv [Preprint]. 2025 Feb 11:2025.02.10.637451. doi: 10.1101/2025.02.10.637451.

Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics.

Park J, Prokopchuk G, Popchock AR, Hao J, Liao TW, Yan S, Hedman DJ, Larson JD, Walther BK, Becker NA, Basu A, Maher LJ 3rd, Wheeler RJ, Asbury CL, Biggins S, Lukeš J, Ha T.

bioRxiv [Preprint]. 2024 Dec 23:2024.12.22.629997. doi: 10.1101/2024.12.22.629997.

The human RAD52 complex undergoes phase separation and facilitates bundling and end-to-end tethering of RAD51 presynaptic filaments.

Alshareedah I, Pangeni S, Dewan PA, Honda M, Liao TW, Spies M, Ha T.

bioRxiv [Preprint]. 2024 Dec 12:2024.12.09.627445. doi: 10.1101/2024.12.09.627445.

Reliable amplification of highly repetitive or low complexity sequence DNA enabled by superhelicase-mediated isothermal amplification.

Kang J, Rashid F, Murray PJ, Merino-Urteaga R, Gavrilov M, Shang T, Jo W, Ahmed A, Aksel T, Barrick D, Berger JM, Ha T.

bioRxiv [Preprint]. 2024 Nov 29:2024.11.27.625726. doi: 10.1101/2024.11.27.625726

Mechanistic insights into direct DNA and RNA strand transfer and dynamic protein exchange of SSB and RPA.

Tapas Paul, I-Ren Lee, Sushil Pangeni, Fahad Rashid, Olivia Yang, Edwin Antony, James M Berger, Sua Myong, Taekjip Ha

bioRxiv [Preprint]. 2025 Apr 1:2025.04.01.643995. doi: 10.1101/2025.04.01.643995.

Rad52 sorts and stacks Rad51 at the DNA junction to promote homologous recombination

Jaigeeth Deveryshetty, Ayush Mistry, Sushil Pangeni, Mohamed Ghoneim, Monica Tokmina-Lukaszewska, Vikas Kaushik, Angela Taddei, Taekjip Ha, Brian Bothner, Edwin Antony

bioRxiv 2024.11.07.622519. doi: 10.1101/2024.11.07.622519.

A high throughput single molecule platform to study DNA supercoiling effect on protein-DNA interactions

Huijin Lee, Jihee Hwang, Fahad Rashid, James A London, Richard Fishel, James M Berger, Sua Myong, Taekjip Ha,

bioRxiv 2024.10.24.620099. doi: 10.1101/2024.10.24.620099.

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

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

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

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)

A genetically encoded fluorescent tRNA is active in live-cell protein synthesis

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 

Nucleic Acids Research 45, 4081-4093 (2017)

Notch-Jagged complex structure implicates a catch bond in tuning ligand sensitivity

V. C. Luca, B.C. Kim, C. Ge, S. Kakuda, D. Wu, M. Roein-Peikar, R. S. Haltiwanger, C. Zhu, T. Ha and K. C. Garcia 

Science 355, 1320-1324 (2017)

Flipping nanoscopy on its head

J. Xiao and T. Ha 

Science 355, 582-584(2017)

Growth factor rattled out of its cage

T. Ha 

Nature 542, 40-41 (2017)

Probing single helicase dynamics on long nucleic acids through fluorescence-force measurements

C. T. Lin and T. Ha 

Methods in Molecular Biology, 1486, 295-316 (2017)

Single-molecule imaging reveals the translocation and DNA looping dynamics of hepatitis C virus NS3 helicase

C. T. Lin, F. Tritschler, K. S. Lee, M. Gu, C. M. Rice and T. Ha 

Protein Science 26, 1391-1403 (2017)

Mapping cell surface adhesion by rotational tracking and adhesion footprinting

T. S. Li, T. Ha and Y. R. Chemla 

Scientific Reports 7, 44502 (2017)

Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes

S. C. Abeysirigunawardena, H. Kim, J. Lai, K. Ragunathan, M. C. Rappe, Z. Luthey-Schulten, T. Ha and S. A. Woodson

 Nature Comm., 8:492 (2017)

Transition folding in Mg2+ and transition metals activates Twister ribozyme

S. Panja, B. Hua, D. Zegarra, T. Ha and S. A. Woodson 

Nature Chem. Biol. 13, 1109-1114 (2017)

Visualization of helicase dynamics using fluorescence localization and optical trapping

C. T. Lin and T. Ha 

Methods in Enzymology, 582, 121-136 (2017)

Sphingolipids facilitate age asymmetry of membrane proteins in dividing yeast cells

P. Singh, S. K. Ramachandra, J, Zhu, B. C. Kim, D. Biswas, T. Ha, P. A. Iglesias and R. Li

 Mol. Biol. Cell 18, 2712-2722 (2017)

Single-cell analysis of early antiviral gene expression reveals a determinant of stochastic IFNB1 expression

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 

Integrative Biology 9, 857-867 (2017)

Voltage-Gated Sodium Channels Assemble and Gate as Dimers

J. Clatot, M. Hoshi, X. Wan, H. Liu, A. Jain, K. Shinlapawittayatorn, C. Marionneau, E. Ficker, T. Ha and I. Deschenes 

Nature Comm. 8:2077 (2017)

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super-resolution

J. Fei, M. Jadaliha, T.S. Harmon, I.T.S. Li, B. Hua, Q. Hao, A.S. Holehouse, M. Reyer, Q. Sun, S.M. Freier, R.V. Pappu, K.V. Prasanth and T. Ha 

Journal of Cell Science 130, 4180-4192 (2017)

Structural dynamics of potassium channel gating revealed by single molecule FRET

S. Wang, R. Vafabakhsh, W.F. Borschel, T. Ha and C.G. Nichols 

Nature Structural & Molecular Biology 23, 31-36 (2016)

Effect of Cytosine Modifications on DNA Flexibility and Nucleosome Mechanical Stability

T. Ngo, J. Yoo, Q. Dai, Q. Zhang, C. He, A. Aksimentiev and T. Ha 

Nature Communications 7:10813 (2016)

Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

J. Yoo, H. Kim, A. Aksimentiev and T. Ha 

Nature Communications 7:11045 (2016)

Probing nature’s nanomachines one molecule at a time

T. Ha 

Biophysical Journal 110, 1004-7 (2016)

Ultrasensitivity of cell adhesion to the presence of mechanically strong ligands

M. Roein-Peikar, Q. Xu, X. Wang and T. Ha 

Physical Review X 6, 011001 (2016)

Plantazolicin is an ultra-narrow spectrum antibiotic that targets Bacillus anthracis membrane

K. J. Molohon, P. M. Blair, S. Park, J. R. Doroghazi, T. Maxson, J. R. Hershfield, K. M. Flatt, N. E. Schroeder, T. Ha, and D. A. Mitchell 

ACS Infectious Disease 2, 207-220 (2016)

 Single-molecule analysis of lipid-protein interactions in crude cell lysates

E. Arauz, V. Aggarwal, A. Jain, T. Ha and J. Chen 

Analytical Chemistry 88; 4269-76 (2016)

Natural antisense RNA promotes 3’ end processing and maturation of MALAT1 lncRNA

X. Zong, S. Nakagawa, S. Freier, J. Fei, T. Ha, S. Prasanth and K. Prasanth

 Nucleic Acids Research 44, 2898-908 (2016)

Constructing modular and universal single molecule tension sensor using protein G to study mechano-sensitive receptors

X. Wang, Z. Rahil, I.T.S. Li, F. Chowdhury, D.E. Leckband, Y.C. Chemla and T. Ha 

Scientific Reports 6:21584 (2016)

Spider silk peptide is a compact, linear nano-spring ideal for intracellular tension sensing

M.D. Brenner, R. Zhou, D.E. Conway, L. Lanzano, E. Gratton, M.A. Schwartz and T. Ha 

Nano Letters 16, 2096-2102 (2016)

Rupture force of cell adhesion ligand tethers modulates biological activities of a cell-laden hydrogel

M.K. Lee, J. Park, X. Wang, M. Roein-Peikar, E. Ko, E. Qin, J.H. Lee, T. Ha and H. Kong 

Chemical Communications 52, 4757-60 (2016)

A chemical controller of SNARE-driven membrane fusion that primes vesicles for Ca2+-triggered millisecond exocytosis

P. Heo, Y. Yang, K. Y. Han, B. Kong, J. H. Shin, Y. Jung, C. Jeong, J. Shin, Y. K. Shin, T. Ha and D. H. Kweon 

J. Am. Chem. Soc. 138, 4512-21 (2016)

Defining single molecular forces required for Notch activation using nano yoyo

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

 Nano Letters 16,  3892-7 (2016)

The light side of the force

A. Basu and T. Ha 

eLife, 5, e14274 (2016)

Ebola virus does not induce stress granule formation during infection and sequesters stress granule proteins within viral inclusions

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

 J. Virology 90, 7268-84 (2016)

In Planta Single-Molecule Pull-down (SiMPull) Reveals Tetrameric Stoichiometry of HD-ZIPIII: LITTLE ZIPPER Complexes

A. Husbands, V. Aggarwal, T. Ha and M. Timmermans 

Plant Cell 28, 1783-94 (2016)

Nanoscale mechanics guides cellular decision making

Z. Rahil, S. Pedron, X. Wang, T. Ha, B. Harley and D. Leckband 

Integrative Biology, 8:929-35 (2016)

Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9

D. Singh, S. Sternberg, J. Fei, J. A. Doudna and T. Ha 

Nature Communications 7, 12778 (2016)

Single-molecule fluorescence microscopy of native macromolecular complexes

V. Aggarwal and T. Ha 

Curr. Opin. Struct. Biol. 41, 225-232 (2016)

Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility

T. Ngo, Q. Zhang, R. Zhou, J. G. Yodh and T. Ha 

Cell 160, 1135-1144 (2015)

Dynamic growth and shrinkage govern the pH dependence of RecA filament stability

S. H. Kim, J. Park, C. Joo, D. Kim and T. Ha 

PLoS One 10:e0115611 (2015)

Determination of in vivo target search kinetics of regulatory noncoding RNA

J. Fei, D. Singh, Q. Zhang, S. Park, D. Balasubramanian, I. Golding, C. K. Vanderpool and T. Ha 

Science 347, 1371-1374 (2015)

Distinct mechanisms regulating mechanical force-induced Ca2+ signals at the plasma membrane and the endoplasmic reticulum in human mesenchymal stem cells

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 

eLife 4, e04876 (2015)

Direct observation of structure-function relationship in a nucleic acid processing enzyme

M. J. Comstock, K.D. Whitley, H. Jia, T.M. Lohman, T. Ha and Y. R. Chemla 

Science 348, 352-354 (2015)

Engineering of a superhelicase through conformational control

S. Arslan, R. Khafizov, C. D. Thomas, Y. R. Chemla and T. Ha 

Science 348, 344-347 (2015)

Nucleosomes undergo slow spontaneous gaping

T. Ngo and T. Ha 

Nucleic Acids Research 43, 3964-3971 (2015)

The preRC protein ORCA Organizes Heterochromatin by Assembling Histone H3 Lysine 9 Methyltransferases on Chromatin

S. Giri, V. Aggarwal, J. Pontis, Z. Shen, A. Chakraborty, A. Khan, C. Mizzen, K. Prasanth, S. Ait-Si-Ali, T. Ha and S. Prasanth

 eLife 4, e06496 (2015)

Dual-color three-dimensional STED microscopy with a single high-repetition-rate laser

K. Y. Han and T. Ha 

Optics Letters 40, 2653-2656 (2015)

BEND3 represses rDNA transcription by stabilizing a NoRC component  via UPS21 deubiquitinase

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 

PNAS 112, 8338-8343 (2015)

A parameter estimation method for fluorescence lifetime data

D. Sewell, H. Kim, T. Ha and P. Ma 

BMC Res Notes 9;8, 230 (2015)

Single molecular force across single integrins dictates cell spreading

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 

Integrative Biology 7, 1265-1271 (2015)

Allosteric regulation of E-cadherin adhesion

N. Shashikanth, Y. I. Petrova, S. Park, J. Chekan, S. Maiden, M. Spano, T. Ha, B. M. Gumbiner and D. E. Leckband 

J. Biol. Chem. 290, 21749-21761 (2015)

KSHV vIRF4 perturbs the G1-S cell cycle progression via deregulation of cyclin D1

H. R. Lee, J. Mitra, S. J. Gao, T. K. Oh, M. Kim, T. Ha and J. U. Jung 

J. Virology 90, 1139-43 (2015)

Effect of DNA replication on transcriptional noise

J. R. Peterson, J. A. Cole, J. Fei, T. Ha and Z. Luthey-Schulten

 PNAS 112, 15886-15891 (2015)       

Tandem “Spinach” Array for mRNA Imaging in Living Bacterial Cells

J. Zhang, J. Fei, B. J. Leslie, K. Y. Han, T. E. Kuhlman and T. Ha 

Scientific Reports 5:17295 (2015)

Integrin molecular tension within motile focal adhesions

X. Wang, J. Sun, Q. Xu, F. Chowdhury, M. Roein-Peikar, Y. Wang and T. Ha 

Biophysical Journal 109, 2259-2267 (2015)

Crosstalk between the cGAS DNA Sensor and Beclin-1 Autophagy Protein Shapes Innate Antimicrobial Immune Responses

Q. Liang, G. J. Seo, Y. J. Choi, M.-J. Kwak, J. Ge, M. A. Rodgers, M. Shi, B. J. Leslie, K.-P. Hopfner, T. Ha, B.-H. Oh, and J. U. Jung 

Cell Host & Microbe 15:2, 228-238 (2014)

Relaxed rotational and scrunching changes in P266L mutant of T7 RNA polymerase reduces short abortive RNAs while delaying transition into elongation

G.-Q. Tang, D. Nandakumar, R. P. Bandwar1, K. S. Lee, R. Roy, T. Ha and S. S. Patel 

PLoS One 9:e91859 (2014)

Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase

S. Syed, M. Pandey, S. S. Patel, and T. Ha 

Cell Reports 6, 1–9 (2014)

Structural mechanisms of PriA-mediated DNA replication restart

B. Bhattacharyya, N. P. George, T. M. Thurmes, R. Zhou, N. Jani, S. R. Wessel, S. J. Sandler, T. Ha and J. L. Keck 

PNAS 111:, 1373-1378 (2014)

Single molecule analysis of Thermus thermophiles SSB protein dynamics on single-stranded DNA

J. Zhang, R. Zhou, J. Inoue, T. Mikawa and T. Ha 

Nucleic Acids Research 42, 3821-32 (2014)

Kaposi's sarcoma-associated herpesvirus viral interferon regulatory factor 4 (vIRF4) targets expression of cellular IRF4 and the Myc gene to facilitate lytic replication

H. Lee, S. Doganay, B. Chung, Z. Toth, K. Brulois, S. Lee, Z. Kanketanyeva, P. Feng, T. Ha, and J. U. Jung 

J. Virology, 88, 2183-94 (2014)

Protein-guided RNA dynamics during early ribosome assembly

H. Kim, S. C. Abeysirigunawardena, K. Chen, M. Mayerle, K. Ragunathan, Z. Luthey-Schulten, T. Ha and S. A. Woodson 

Nature 506, 334-8 (2014)

A dynamic look at DNA unwinding by a replicative helicase

S. J. Lee, S. Syed , E. J. Enemark , S. Schuck , A. Stenlund , T. Ha and L. Joshua-Tor 

Proc. Natl. Acad. Sci. USA, 111, E827-35 (2014)

Towards a computational model of a methane producing archaeum

J. Peterson, P. Labhsetwar, J. R. Ellermeier, P.R.A. Kohler, A. Jain, T. Ha, W. W. Metcalf, and Z. A. Luthey-Schulten 

Archaea 2014:898453 (2014)

Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA

R. Zhou, J. Zhang, M. L. Bockman, V. A. Zakian and T. Ha

 eLife 3:e02190 (2014)

Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer

K. S. Lee, A. B. Marciel, A. G. Kozlov, C. M. Schroeder, T. M. Lohman and T. Ha 

J. Mol. Bio., 426, 2413-21 (2014)

A coarse-grained model of unstretched single-stranded DNA derived from atomistic simulation and single-molecule experiment

C. Maffeo, T. Ngo, T. Ha, A. Aksimentiev 

J. Chem. Theory Comput 10, 2891–2896 (2014)

Matrix softness regulates plasticity of tumor-repopulating cells via H3K9 demethylation and Sox2 expression

Y. Tan, A. Tajik, J. Chen, Q. Jia, F. Chowdhury, L. Wang, J. Chen, S. Zhang, Y. Hong, H. Yi, D. 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 

Nature Communications 5:4619, doi:10.1038/ncomms5619 (2014)

Designing a nine cysteine-less DNA packaging motor from bacteriophage T4 reveals new insights into ATPase structure and function

K. Kondabagil, L. Dai, R. Vafabakhsh, T. Ha, B. Draper and V. Rao 

Virology, 468-470, 660-668 (2014)

Single molecule packaging initiation in real-time by a viral DNA packaging machine from bacteriophage T4

R. Vafabakhsh, K. Kondabagil, T. Earnest, K. Lee, Z. Zhang, L. Dai, K. A. Dahmen, V. B. Rao and T. Ha 

Proc. Natl. Acad. Sci. USA 111, 15096-15101 (2014)

Targeting DNA G-Quadruplexes with Helical Small Molecules

S. Müller, K. Laxmi-Reddy, P. V. Jena, B. Baptiste, Z. Dong, F. Godde, T. Ha, R. Rodrguez, S. Balasubramanian and I. Huc 

ChemBioChem 15, 2563-2570 (2014)

Single Molecule Methods Leap Ahead

T. Ha 

Nature Methods 11, 1015-1018 (2014)

An improved single molecule passivation method for single molecule studies

B. Hua, K.Y. Han, R. Zhou, H. Kim, X. Shi, S. C. Abeysirigunawardena, A. Jain, D. Singh, V. Aggarwal, S. A. Woodson and T. Ha 

Nature Methods 11, 1233-1236 (2014)

Cooperative conformational transitions keep RecA filament active during ATPase cycle

S. H. Kim, K. Ragunathan, J. Park, C. Joo, D. Kim and T. Ha 

J. Am. Chem. Soc. 136:42, 14796-14800 (2014)

Single-molecule pull-down (SiMPull) for new-age biochemistry

V. Aggarwal and T. Ha 

Bioessay, doi: 10.1002/bies.201400090 (2014)

Stoichiometry and assembly of mTOR complexes revealed by single-molecule pull-down

A. Jain, E. Arauz, V. Aggarwal, N. Ikon, J. Chen and T. Ha 

Proc. Natl. Acad. Sci. USA 111, 17833-17838 (2014)

A price to pay for relaxed substrate specificity: A comparative kinetic analysis of the class II lanthipeptide synthetases, ProcM and HalM2

C. J. Thibodeaux, T. Ha and W. A. van der Donk 

J. Am. Chem. Soc. 136:50, 17513-17529 (2014)

The SOSS1 single-stranded DNA binding complex promotes DNA end resection in concert with Exo1

S. H. Yang, R. Zhou, J. Campbell, J. Chen, T. Ha and T.T. Paull 

EMBO J. 32, 126-139 (2013)

Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation

D. N. Ermolenko, P. V. Cornish, T. Ha and H. F. Noller 

RNA 19, 158-166 (2013)

The telomere capping complex CST has an unusual stoichiometry, makes multipartite interaction with G-tails, and unfolds higher-order G-tail structures

N. F. Lue, R. Zhou, L. Chico, N. Mao, O. Steinberg-Neifach and T. Ha 

PLoS Genetics 9, e1003145 (2013)

Single molecule nanometry for biological physics

H. Kim and T. Ha 

Reports on Progress in Physics 76, 016601 (2013)

Fusion pore formation and expansion induced by Ca2+ and synaptotagmin 1

Y. Lai, J. Diao, Y. Liu, Y. Ishitsuka, Z. Su, K. Schulten, T. Ha and Y.K. Shin 

PNAS 110, 1333-1338 (2013)

Defining Single Molecular Forces Required to Activate Integrin and Notch Signaling

X. Wang and T. Ha 

Science 340, 991-994 (2013)

Direct imaging of single UvrD helicase dynamics on long single-stranded DNA

K. S. Lee, H. Balci, H. Jia, T. M. Lohman and T. Ha 

Nature Commun. 4, 1878 (2013)

Single molecule FRET reveals the native state dynamic of the IκBα ankyrin repeat domain

J. A. Lamboy, H. Kim, H. Dembinski, T. Ha and E. A. Komives 

J. Mol. Biol. 425, 2578-2590 (2013)

A dendritic single-molecule fluorescent probe that is monovalent, photostable, and minimally blinking

S. K. Yang, X. Shi, S. Park, T. Ha, S. C. Zimmerman 

Nature Chem. 5, 692-697 (2013)

PriC-mediated DNA replication restart requires PriC complex formation with the single-stranded DNA-binding protein

S. R. Wessel, A. H. Marceau, S. C. Massoni, R. Zhou, T. Ha, S. J. Sandler and J. L. Keck 

J. Biol. Chem. 288, 17569-17578 (2013)

Molecular mechanism of sequence-dependent stability of RecA filament

S. H. Kim, C. Joo, T. Ha and D. Kim 

Nucleic Acids Research 41, 7738-7744 (2013)

ATPase-driven oligomerization of RIG-I on RNA allows optimal activation of type-I interferon

J. Patel, A. Jain, Y.Y. Chou, A. Baum, T. Ha and A. Garcia-Sastre 

EMBO Reports 14, 780-787 (2013)

Single molecule approaches embrace molecular cohorts

T. Ha 

Cell 154, 723-726 (2013)

Understanding the photophysics of the Spinach-DFHBI RNA aptamer-fluorogen complex to improve live cell RNA imaging

K. Y. Han, B. Leslie, J. Fei, J. Zhang, and T. Ha 

J. Am. Chem. Soc 135, 19033-19038 (2013)

Watching DNA breath one molecule at a time

J. Fei and T. Ha

 Proc. Natl. Acad. Sci. USA, 110, 17173-17174 (2013)

Antiparallel EmrE exports drugs by exchanging between asymmetric structures

E. A. Morrison, G. T. DeKoster, S. Dutta, R. Vafabakhsh, M. Charkson, A. Bahl, D. Kern, T. Ha and K. A. Henzler-Wildman 

Nature 481, 45-50 (2012)

Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging

T. Ha and P. Tinnefeld 

Annual Review of Physical Chemistry 63, 595-617 (2012)

Single-molecule views of protein movement on single-stranded DNA

T. Ha, A. G. Kozlov and T. M. Lohman 

Annual Review of Biophysics 41, 295-319 (2012)

Single-molecule pull-down for studying protein interactions

A. Jain, R. Liu, Y.K. Xiang and T. Ha 

Nature Protocols 7, 445–452 (2012)

Quantitative fluorescence labeling of aldehyde-tagged proteins for single-molecule imaging

X. Shi, Y. Jung, L.J. Lin, C. Liu, C. Wu, I.K.O. Cann and T. Ha 

Nature Methods 9, 499-503 (2012)

A single vesicle-vesicle fusion assay for in vitro studies of SNAREs and accessory proteins

J. Diao, Y. Ishitsuka, H.K. Lee, C. Joo, Z. Su, S. Syed, Y.K. Shin, T.Y. Yoon and T. Ha 

Nature Protocols 7, 912-934 (2012)

Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Go simulations

K. Chen, J. Eargle, J. Lai, H. Kim, S. Abeysirigunawardena, M. Mayerle, S.A. Woodson, T. Ha and Z. Luthey-Schulten 

J. Phys. Chem. B 116, 6819-6831(2012)

The influenza A virus PB2, PA, NP and M segments play a pivotal role during genome packaging

Q. Gao, Y.Y. Chou, S. Doganay, R. Vafabakhsh, T. Ha and P. Palese 

J. Virology 86, 7043-51 (2012)

One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis

Y.Y. Chou, R. Vafabakhsh, S. Doğanay, Q. Gao, T. Ha and P. Palese 

PNAS, 109, 9101-9106 (2012)

A rule of seven in Watson-Crick base pairing of mismatched sequences

I. Cisse, H. Kim and T. Ha 

Nature Structural & Molecular Biology 19, 623-627 (2012)

Single-molecule imaging: A collagenase pauses before embarking on a killing spree

G. Lee and T. Ha 

Current Biology 22 (12), R499–R501 (2012)

Dynamic association of ORCA with pre-RC components regulates DNA replication initiation

Z. Shen, A. Chakraborty, A. Jain, S. Giri, T. Ha, K. V. Prasanth and S. G. Prasanth 

Mol. Cell. Biol. 32, 3107-20 (2012)

Elastic coupling between RNA degradation and unwinding by an exoribonuclease

G. Lee, M. Bratkowski, F. Ding, A. Ke and T. Ha 

Science, 336, 1726-1729 (2012)

Extreme bendability of DNA less than 100 base pairs long revealed by single molecule cyclization

R. Vafabakhsh and T. Ha 

Science 337, 1097-1101 (2012)

Dynamics of major histocompatibility complex class I association with the human peptide-loading complex

M.S. Panter, A. Jain, R.M. Leonhardt, T. Ha and P. Cresswell 

J. Biol. Chem. 287, 31172–31184 (2012)

Single-molecule analysis of SSB dynamics on single-stranded DNA

R. Zhou and T. Ha 

Methods Mol. Biol. 922, 85-100 (2012)

A helicase with an extra spring in its step

M. Schlierf and T. Ha 

Cell 151, 244-246 (2012)

RecA filament sliding on DNA facilitates homology search

K. Ragunathan, C. Liu and T. Ha 

eLife 1, e00067 (2012)

Activated GTPase movement on an RNA scaffold drives cotranslational protein targeting

K. Shen, S. Arslan, D. Akopian, T. Ha and S. Shan 

Nature 492, 271-275 (2012)