Our research focuses on uncovering how mechanical forces shape cellular behavior, structural organization, and fate within living systems. These forces are central to processes such as adhesion, migration, and cytoskeletal dynamics, yet remain difficult to visualize with molecular precision. To address this challenge, we developed Tension Points Accumulation for Imaging in Nanoscale Topography (Tension-PAINT), a super-resolution imaging technique that integrates molecular tension probes with the DNA Points Accumulation for Imaging in Nanoscale Topography (DNA-PAINT) platform. This method enables the visualization of pN-scale mechanical events with spatial resolution approaching 25 nm, allowing us to monitor cellular forces in real time.
To support live cell imaging of dynamic mechanical activity, we engineered reversible tPAINT probes that expose hidden DNA docking sites only when subjected to forces above programmable thresholds, typically in the range of 7 to 21 pN. In parallel, we created irreversible probes that permanently reveal their docking sites after force activation, allowing us to record a mechanical force history with enhanced spatial precision at the expense of temporal resolution. Using both probe types, we imaged integrin receptor forces in live human platelets and mouse embryonic fibroblasts, and uncovered spatially regulated mechanotransduction behaviors. Notably, we observed a strong correlation between platelet traction forces at the leading edge and the formation of a dynamic actin-rich ring driven by the Arp2/3 complex. These results demonstrate how mechanical cues are organized in space and time, and how they contribute to cellular decision-making in complex biological environments.
Selected Publications and Manuscripts:
Brockman, J.,‡ Su, H.,‡ Blanchard, A., Duan, Y., Meyer, T., Quach, E., Glazier, R., Bazrafshan, A., Ma, R., Schueder, F., Petrich, B., Jungmann, R., Li, R., Mattheyses, A., Ke, Y., Salaita, K., “Live-cell super-resolved PAINT imaging of pN cellular traction forces”, Nature Methods 2020 (co-first author)
Blanchard, A., J. Comb, D., Brockman, J., Kellner, A., Glazier, R., Su, H., Bazrafshan, A., Bender, R., Chen, W., Quach, E., Li, R., Mattheyses A., Salaita, K., “Turn-key super-resolution mapping of cell receptor force orientation and magnitude using a commercial structured illumination microscope”, Nature Communications 2021, DOI: 11.1038/s41467-021-24602-x
Ma, R., Kellner, A. V., Ma, V. P., Su, H., Deal, B. R., Brockman, J. M., Salaita, K., "DNA probes that store mechanical information reveal transient piconewton forces applied by T cells." Proceedings of the National Academy of Sciences of the United States of America 2019 Aug 20;116(34):16949-16954.
Ma, V. P., Liu, Y., Blanchfield, L., Su, H., Evavold, B. D., Salaita, K., "Ratiometric Tension Probes for Mapping Receptor Forces and Clustering at Intermembrane Junctions." Nano Letters 2016 Jul 13;16(7):4552-9.
RNA and protein molecules form the essential foundation of most biological processes, with their functions closely tied to their spatial distribution and abundance. Fluorescence imaging techniques such as immunofluorescence (IF) and single-molecule fluorescent in situ hybridization (smFISH) have been instrumental in quantifying and spatially mapping these molecules, offering valuable insights into a wide range of biological questions. However, traditional methods are limited by the finite number of fluorophores and secondary antibodies, restricting simultaneous profiling to only a few targets. To overcome this barrier, DNA exchange strategies and signal amplification methods have been introduced, leveraging orthogonal probe binding and rapid probe exchange to enable multiplexed molecular detection. Despite their promise, these methods face persistent technical challenges that have hindered widespread adoption.
In response, we have worked alongside pioneers in DNA nanoscience and spatial biology to develop the next generation of DNA-based multiplex imaging platforms. Our research aims to uncover how the spatial organization of gene and protein expression governs cellular behavior across scales, from single cells to complex tissues. We explored how cells operate within microenvironments where molecular activity is shaped not only by genetic programs but also by spatial inputs from neighboring cells and the extracellular matrix. These spatial patterns play pivotal roles in regulating development, immune function, and disease progression. To systematically capture this biological complexity, we engineered DNA-based imaging technologies for highly scalable and multiplexed visualization of RNA and proteins in both 2D and 3D samples. Our innovations include an in situ signal amplification strategy for sensitive co-detection and a fluidic exchange-free platform for rapid cyclic protein imaging. In collaboration with neurobiologists, pathologists, and bioengineers, we applied these tools to cleared mouse brains, human tonsils, and thick tissue sections, generating spatial molecular maps that reveal how the local environment shapes cellular identity and function.
Selected Publications and Manuscripts:
Su, H.,‡ Sheng, K.,‡ Furman, M., Sarraf, N., George, C., Jeong, J., Hong, F., Ma, K., Gowri, G., Serrata, M., Pihan, G., Yin, P., “Signal amplified wash-free DNA probe exchange enables rapid and scalable spatial protein imaging.” Manuscript in Preparation. (co-first author)
Sheng, K.,‡ Su, H.,‡* Gowri, G., Serrata, M., Furman, M., Jeong, J., Ma, K., Du, L., George, C., Lun, X., Yin, P.,* “ACE Enables Multiscale Highly Multiplexed Biomolecule Imaging with Signal Amplification in Cells and Deep Tissues.” Manuscript in Preparation. (co-first author and co-corresponding author)
Jiang, H.,‡ Walker, L. A.,‡ Li, Y., Duan, B., Niu, X., Hsieh, J. C., Cheng, M. C., Tang, J. P., Athukorala, K., Pan, R., Parlapalli, A., Greene, S., Su, H., Yin, P., Cui, M., Cai, D., “A parallelly distributed microscope and software system for scalable high-throughput multispectral 3D imaging.” BioRxiv 2025.05.31.657163.
Wang, S.,‡ Shin, T-W.,‡ Yoder, H.B., McMillan, R.B., Su, H., Liu, Y., Zhang, C., Leung, K.S., Yin, P., Kiessling, L.L., Boyden, E.S., “Single-shot 20-fold Expansion Microscopy.” Nature Methods, 2025.
Lun, X., Sheng, K., Yu, X., Lam, C-Y., Gowri, G., Serrata M., Zhai, Y., Su, H., Luan, J., Kim, Y., Ingber D., Jackson, H., Yaffe, M., Yin, P., “Signal amplification by cyclic extension enables high-sensitivity single-cell mass cytometry.” Nature Biotechnology 2024:1-11.
Hong, F., Kishi, J., Jeong, J., Saka, S., Su, H., Cepko, C.L., Delgado, R., Yin, P., “Thermal-plex: Fluidic-free, rapid sequential multiplexed imaging with DNA encoded thermal channels.” Nature Methods 2024 Feb;21(2):331-341.
Sarkar, D., Kang, J., Wassie, A.T., Schroeder M.E., Peng, Z., Tarr, T.B., Tang, A., Niederst, E., Young, J.Z., Su, H., Park, D., Yin, P., Tsai, L., Blanpied, T.A., Boyden, E.S., “Expansion Revealing: Decrowding Proteins to Unmask Invisible Brain Nanostructures.” Nature Biomedical Engineering 2022 Sep;6(9):1057-1073.
iii. High-throughput biomolecular force manipulation (Force-jump)
Single-molecule force spectroscopy (SMFS) is a technique that stretches individual tethered molecules using instruments such as atomic force microscopes (AFM) or optical tweezers to study their mechanical behavior under applied force. However, SMFS is inherently sequential and low-throughput, as it measures one molecule at a time. To address this limitation, we developed the polymer force clamp (PFC) and the DNA origami polymer force clamp (OPFC). These tools enable parallel mechanical manipulation of molecules without the need for dedicated SMFS equipment or surface tethering. The first-generation PFC consists of a plasmonic nanorod core surrounded by a thermoresponsive polymer shell. Upon optical heating, the nanorod induces rapid contraction of the polymer, converting light into mechanical work that unfolds target molecules. The magnitude and duration of the applied force can be tuned by adjusting illumination intensity and exposure time, which control the extent and timing of particle contraction. Using single-molecule fluorescence imaging, we demonstrated reproducible mechanical unfolding of DNA hairpins and successfully triggered unfolding in 50 individual particles within one minute, surpassing the throughput of conventional AFM. Building on this platform, we developed the second-generation OPFC, which positions target molecules between a contractile polymer particle and a rigid DNA origami beam. This design allows for tunable force application and high spatial precision. As a demonstration, we measured both steady state and time-resolved (force-jump) mechanical unfolding of DNA hairpins using fluorescence readouts from molecular ensembles. These experimental findings were further supported by computational modeling.
Selected Publications and Manuscripts:
Su, H.,‡ Brockman, J.,‡ Duan, Y.,‡ Sen, N., Chhabra, H., Bazrafshan, A., Blanchard, A., Meyer, T., Andrews, B., Doye, J., Ke, Y., Dyer, R.B., Salaita, K., “Massively parallelized molecular force manipulation with on demand thermal and optical control”, Journal of the American Chemical Society 2021.
Ramey-Ward, A. N., Su, H., Salaita, K., "Mechanical Stimulation of Adhesion Receptors Using Light-Responsive Nanoparticle Actuators Enhances Myogenesis." ACS Applied Materials & Interfaces 2020 Aug 12;12(32):35903-35917.
Zhao, J., Su, H., Vansuch, G. E., Liu, Z., Salaita, K., Dyer, R. B., "Localized Nanoscale Heating Leads to Ultrafast Hydrogel Volume-Phase Transition." ACS Nano 2019 Jan 22;13(1):515-525.
Su, H., ‡ Liu, Z.,‡ Liu, Y., Ma, V. P.-Y., Blanchard, A., Zhao, J., Galior, K., Dyer, R. B., Salaita, K., “Nanoparticle force-clamp for optically controlled mechanical unfolding of DNA”, Nano Letters 2018, 18, 4, 2630-2636.