Taekjip Ha

Taekjip Ha

Bloomberg Distinguished Professor

169 Mergenthaler
Group/Lab Website

Research Interests: Single Molecule and Cell Biophysics

Education: PhD, University of California at Berkeley

The Ha Lab is not taking new PhD students.

Dr. Taekjip Ha is a Bloomberg Distinguished Professor of Biophysics and Biophysical Chemistry, Biophysics, and Biomedical Engineering at Johns Hopkins University School of Medicine. He is also an investigator with the Howard Hughes Medical Institute. He uses sophisticated physical techniques to manipulate and visualize the movements of single molecules to understand basic biological processes involving DNA and other molecules. His study is focused on pushing the limits of single-molecule detection methods to study protein–nucleic acid and protein-protein complexes and the mechanical basis of their interactions and functions – both in vitro and in vivo – that are important for genome maintenance.

Dr. Ha received his undergraduate degree in Physics, from Seoul National University, Seoul, Republic of Korea in 1990.  He earned his Ph.D. In Physics from the University of Berkeley in 1996. After postdoctoral training at Stanford University, he was a Physics professor at University of Illinois at Urbana-Champaign for fifteen years until 2015.

Dr. Ha serves as a member of Editorial Boards for Science, Cell, eLife, PRX, Structure, PCCP, Physical Biology and Cancer Convergence. He is a member of the National Academy of Science and an elected fellow of the American Academy of Arts and Sciences.

Single Molecule Biophysics

Our research is focused on pushing the limits of single-molecule detection methods to study complex biological systems. We develop state-of-the-art biophysical techniques (e.g., multicolor fluorescence, super-resolution imaging, combined force and fluorescence spectroscopy, vesicular encapsulation, single-molecule pull-down) and applies them to study diverse protein-nucleic acid and protein-protein complexes, and mechanical perturbation and response of these systems both in vitro and in vivo.

Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding. (I. C. Okafor, D. Singh, Y. Wang, M. Jung, H. Wang, J. Mallon, S. Bailey, J. K. Lee, T. Ha), In Nucleic Acids Res., Nucleic Acids Res., 2019. 

Streamlining effects of extra telomeric repeat on telomeric DNA folding revealed by fluorescence-force spectroscopy. (J. Mitra, T. Ha), In Nucleic Acids Res., Nucleic Acids Res., 2019. 

Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy. (J. Mitra, M. A. Makurath, T. T. M. Ngo, A. Troitskaia, Y. R. Chemla, T. Ha), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2019. 

Nanomechanics and co-transcriptional folding of Spinach and Mango. (J. Mitra, T. Ha), In Nat Commun, Nat Commun, 2019. 

Junction resolving enzymes use multivalency to keep the Holliday junction dynamic. (R. Zhou, O. Yang, A. C. Déclais, H. Jin, G. H. Gwon, A. D. J. Freeman, Y. Cho, D. M. J. Lilley, T. Ha), In Nat. Chem. Biol., Nat. Chem. Biol., 2019. 

 Hexameric helicase G40P unwinds DNA in single base pair steps. (M. Schlierf, G. Wang, X. S. Chen, T. Ha), In Elife, Elife, 2019. 

Mimicking Co-Transcriptional RNA Folding Using a Superhelicase. (B. Hua, S. Panja, Y. Wang, S. A. Woodson, T. Ha), In J. Am. Chem. Soc., J. Am. Chem. Soc., 2018. 

Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis. (D. Singh, Y. Wang, J. Mallon, O. Yang, J. Fei, A. Poddar, D. Ceylan, S. Bailey, T. Ha), In Nat. Struct. Mol. Biol., Nat. Struct. Mol. Biol., 2018. 

Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a). (D. Singh, J. Mallon, A. Poddar, Y. Wang, R. Tippana, O. Yang, S. Bailey, T. Ha), In Proc. Natl. Acad. Sci. U.S.A., Proc. Natl. Acad. Sci. U.S.A., 2018. 

Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution. (H. R. Koh, R. Roy, M. Sorokina, G. Q. Tang, D. Nandakumar, S. S. Patel, T. Ha), In Mol. Cell, Mol. Cell, 2018.  

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution. (J. Fei, M. Jadaliha, T. S. Harmon, I. T. S. Li, B. Hua, Q. Hao, A. S. Holehouse, M. Reyer, Q. Sun, S. M. Freier, R. V. Pappu, K. V. Prasanth, T. Ha), In J. Cell. Sci., J. Cell. Sci., 2017. 

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).

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,” Science347, 1371-1374 (2015).

T. Ngo, Q. Zhang, R. Zhou, J. G. Yodh and T. Ha, “Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility,” Cell160, 1135–1144 (2015).

X. Wang and T. Ha, “Defining Single Molecular Forces Required to Activate Integrin and Notch Signaling,” Science340, 991–994 (2013).

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).

A. Jain, R. Liu, B. Ramani, E. Arauz, Y. Ishitsuka, K. Ragunathan, J. Park, J. Chen, Y. K. Xiang and T. Ha, “Probing cellular protein complexes using single-molecule pull-down,” Nature473, 484–488  (2011).