Academic Appointments

  • Basic Life Science Research Associate, Bioengineering

All Publications

  • Optical control of fast and processive engineered myosins in vitro and in living cells. Nature chemical biology Ruijgrok, P. V., Ghosh, R. P., Zemsky, S. n., Nakamura, M. n., Gong, R. n., Ning, L. n., Chen, R. n., Vachharajani, V. T., Chu, A. E., Anand, N. n., Eguchi, R. R., Huang, P. S., Lin, M. Z., Alushin, G. M., Liphardt, J. T., Bryant, Z. n. 2021


    Precision tools for spatiotemporal control of cytoskeletal motor function are needed to dissect fundamental biological processes ranging from intracellular transport to cell migration and division. Direct optical control of motor speed and direction is one promising approach, but it remains a challenge to engineer controllable motors with desirable properties such as the speed and processivity required for transport applications in living cells. Here, we develop engineered myosin motors that combine large optical modulation depths with high velocities, and create processive myosin motors with optically controllable directionality. We characterize the performance of the motors using in vitro motility assays, single-molecule tracking and live-cell imaging. Bidirectional processive motors move efficiently toward the tips of cellular protrusions in the presence of blue light, and can transport molecular cargo in cells. Robust gearshifting myosins will further enable programmable transport in contexts ranging from in vitro active matter reconstitutions to microfabricated systems that harness molecular propulsion.

    View details for DOI 10.1038/s41589-021-00740-7

    View details for PubMedID 33603247

  • Engineered miniature CRISPR-Cas system for mammalian genome regulation and editing. Molecular cell Xu, X., Chemparathy, A., Zeng, L., Kempton, H. R., Shang, S., Nakamura, M., Qi, L. S. 2021


    Compact and versatile CRISPR-Cas systems will enable genome engineering applications through high-efficiency delivery in a wide variety of contexts. Here, we create an efficient miniature Cas system (CasMINI) engineered from the type V-F Cas12f (Cas14) system by guide RNA and protein engineering, which is less than half the size of currently used CRISPR systems (Cas9 or Cas12a). We demonstrate that CasMINI can drive high levels of gene activation (up to thousands-fold increases), while the natural Cas12f system fails to function in mammalian cells. We show that the CasMINI system has comparable activities to Cas12a for gene activation, is highly specific, and allows robust base editing and gene editing. We expect that CasMINI can be broadly useful for cell engineering and gene therapy applications ex vivo and in vivo.

    View details for DOI 10.1016/j.molcel.2021.08.008

    View details for PubMedID 34480847

  • CRISPR technologies for precise epigenome editing. Nature cell biology Nakamura, M., Gao, Y., Dominguez, A. A., Qi, L. S. 2021; 23 (1): 11–22


    The epigenome involves a complex set of cellular processes governing genomic activity. Dissecting this complexity necessitates the development of tools capable of specifically manipulating these processes. The repurposing of prokaryotic CRISPR systems has allowed for the development of diverse technologies for epigenome engineering. Here, we review the state of currently achievable epigenetic manipulations along with corresponding applications. With future optimization, CRISPR-based epigenomic editing stands as a set of powerful tools for understanding and controlling biological function.

    View details for DOI 10.1038/s41556-020-00620-7

    View details for PubMedID 33420494

  • Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells. Nature communications Nakamura, M., Srinivasan, P., Chavez, M., Carter, M. A., Dominguez, A. A., La Russa, M., Lau, M. B., Abbott, T. R., Xu, X., Zhao, D., Gao, Y., Kipniss, N. H., Smolke, C. D., Bondy-Denomy, J., Qi, L. S. 2019; 10 (1): 194


    Repurposed CRISPR-Cas molecules provide a useful tool set for broad applications of genomic editing and regulation of gene expression in prokaryotes and eukaryotes. Recent discovery of phage-derived proteins, anti-CRISPRs, which serve to abrogate natural CRISPR anti-phage activity, potentially expands the ability to build synthetic CRISPR-mediated circuits. Here, we characterize a panel of anti-CRISPR molecules for expanded applications to counteract CRISPR-mediated gene activation and repression of reporter and endogenous genes in various cell types. We demonstrate that cells pre-engineered with anti-CRISPR molecules become resistant to gene editing, thus providing a means to generate "write-protected" cells that prevent future gene editing. We further show that anti-CRISPRs can be used to control CRISPR-based gene regulation circuits, including implementation of a pulse generator circuit in mammalian cells. Our work suggests that anti-CRISPR proteins should serve as widely applicable tools for synthetic systems regulating the behavior of eukaryotic cells.

    View details for PubMedID 30643127

  • CRISPR-mediated live imaging of genome editing and transcription. Science (New York, N.Y.) Wang, H. n., Nakamura, M. n., Abbott, T. R., Zhao, D. n., Luo, K. n., Yu, C. n., Nguyen, C. M., Lo, A. n., Daley, T. P., La Russa, M. n., Liu, Y. n., Qi, L. S. 2019


    We report a robust, versatile approach named CRISPR Live-cell fluorescent in situ hybridization (LiveFISH) using fluorescent oligos for genome tracking in broad cell types including primary cells. An intrinsic stability switch of CRISPR guide RNAs enables LiveFISH to accurately detect chromosomal disorders such as Patau Syndrome in prenatal amniotic fluid cells and track multiple loci in human T lymphocytes. In addition, LiveFISH tracks the real-time movement of DNA double-strand breaks induced by CRISPR-Cas9-mediated editing and consequent chromosome translocations. Finally, combining Cas9 and Cas13 systems, LiveFISH allows for simultaneous visualization of genomic DNA and RNA transcripts in living cells. The LiveFISH approach enables real-time live imaging of DNA and RNA during genome editing, transcription, and rearrangements in single cells.

    View details for DOI 10.1126/science.aax7852

    View details for PubMedID 31488703

  • Remote control of myosin and kinesin motors using light-activated gearshifting. Nature nanotechnology Nakamura, M., Chen, L., Howes, S. C., Schindler, T. D., Nogales, E., Bryant, Z. 2014; 9 (9): 693-697


    Cytoskeletal motors perform critical force generation and transport functions in eukaryotic cells. Engineered modifications of motor function provide direct tests of protein structure-function relationships and potential tools for controlling cellular processes or for harnessing molecular transport in artificial systems. Here, we report the design and characterization of a panel of cytoskeletal motors that reversibly change gears-speed up, slow down or switch directions-when exposed to blue light. Our genetically encoded structural designs incorporate a photoactive protein domain to enable light-dependent conformational changes in an engineered lever arm. Using in vitro motility assays, we demonstrate robust spatiotemporal control over motor function and characterize the kinetics of the optical gearshifting mechanism. We have used a modular approach to create optical gearshifting motors for both actin-based and microtubule-based transport.

    View details for DOI 10.1038/nnano.2014.147

    View details for PubMedID 25086603

  • Engineering myosins for long-range transport on actin filaments NATURE NANOTECHNOLOGY Schindler, T. D., Chen, L., Lebel, P., Nakamura, M., Bryant, Z. 2014; 9 (1): 33-38


    Cytoskeletal motors act as cargo transporters in cells and may be harnessed for directed transport applications in molecular detection and diagnostic devices. High processivity, the ability to take many steps along a track before dissociating, is often a desirable characteristic because it allows nanoscale motors to transport cargoes over distances on the scale of micrometres, in vivo and in vitro. Natural processive myosins are dimeric and use internal tension to coordinate the detachment cycles of the two heads. Here, we show that processivity can be enhanced in engineered myosins using two non-natural strategies designed to optimize the effectiveness of random, uncoordinated stepping: (1) the formation of three-headed and four-headed myosins and (2) the introduction of flexible elements between heads. We quantify improvements using systematic single-molecule characterization of a panel of engineered motors. To test the modularity of our approach, we design a controllably bidirectional myosin that is robustly processive in both forward and backward directions, and also produce the fastest processive cytoskeletal motor measured so far, reaching a speed of 10 µm s(-1).

    View details for DOI 10.1038/NNANO.2013.229

    View details for Web of Science ID 000329315000011

    View details for PubMedID 24240432

  • Engineering controllable bidirectional molecular motors based on myosin NATURE NANOTECHNOLOGY Chen, L., Nakamura, M., Schindler, T. D., Parker, D., Bryant, Z. 2012; 7 (4): 252-256


    Cytoskeletal motors drive the transport of organelles and molecular cargoes within cells and have potential applications in molecular detection and diagnostic devices. Engineering molecular motors with controllable properties will allow selective perturbation of mechanical processes in living cells and provide optimized device components for tasks such as molecular sorting and directed assembly. Biological motors have previously been modified by introducing activation/deactivation switches that respond to metal ions and other signals. Here, we show that myosin motors can be engineered to reversibly change their direction of motion in response to a calcium signal. Building on previous protein engineering studies and guided by a structural model for the redirected power stroke of myosin VI, we have constructed bidirectional myosins through the rigid recombination of structural modules. The performance of the motors was confirmed using gliding filament assays and single fluorophore tracking. Our strategy, in which external signals trigger changes in the geometry and mechanics of myosin lever arms, should make it possible to achieve spatiotemporal control over a range of motor properties including processivity, stride size and branchpoint turning.

    View details for DOI 10.1038/NNANO.2012.19

    View details for Web of Science ID 000302578300012

    View details for PubMedID 22343382

    View details for PubMedCentralID PMC3332125

  • Real-time observation of RecA filament dynamics with single monomer resolution CELL Joo, C., McKinney, S. A., Nakamura, M., Rasnik, I., Myong, S., Ha, T. 2006; 126 (3): 515-527


    RecA and its homologs help maintain genomic integrity through recombination. Using single-molecule fluorescence assays and hidden Markov modeling, we show the most direct evidence that a RecA filament grows and shrinks primarily one monomer at a time and only at the extremities. Both ends grow and shrink, contrary to expectation, but a higher binding rate at one end is responsible for directional filament growth. Quantitative rate determination also provides insights into how RecA might control DNA accessibility in vivo. We find that about five monomers are sufficient for filament nucleation. Although ordinarily single-stranded DNA binding protein (SSB) prevents filament nucleation, single RecA monomers can easily be added to an existing filament and displace SSB from DNA at the rate of filament extension. This supports the proposal for a passive role of RecA-loading machineries in SSB removal.

    View details for DOI 10.1016/j.cell.2006.06.042

    View details for Web of Science ID 000239883400012

    View details for PubMedID 16901785