Honors & Awards

  • National Research Service Award, National Heart, Lung, And Blood Institute of the National Institutes of Health (2018 - 2019)
  • School of Medicine Dean's Postdoctoral Fellowship, Stanford University (2017 - 2018)

Education & Certifications

  • Postdoctoral Research Fellow, Stanford University School of Medicine, Biochemistry (2019)
  • Doctor of Philosophy, Harvard University, Biophysics (2017)
  • Bachelor of Science, California Institute of Technology, Physics (2010)

All Publications

  • beta-Cardiac myosin hypertrophic cardiomyopathy mutations release sequestered heads and increase enzymatic activity. Nature communications Adhikari, A. S., Trivedi, D. V., Sarkar, S. S., Song, D., Kooiker, K. B., Bernstein, D., Spudich, J. A., Ruppel, K. M. 2019; 10 (1): 2685


    Hypertrophic cardiomyopathy (HCM) affects 1 in 500 people and leads to hyper-contractility of the heart. Nearly 40 percent of HCM-causing mutations are found in human beta-cardiac myosin. Previous studies looking at the effect of HCM mutations on the force, velocity and ATPase activity of the catalytic domain of human beta-cardiac myosin have not shown clear trends leading to hypercontractility at the molecular scale. Here we present functional data showing that four separate HCM mutations located at the myosin head-tail (R249Q, H251N) and head-head (D382Y, R719W) interfaces of a folded-back sequestered state referred to as the interacting heads motif (IHM) lead to a significant increase in the number of heads functionally accessible for interaction with actin. These results provide evidence that HCM mutations can modulate myosin activity by disrupting intramolecular interactions within the proposed sequestered state, which could lead to hypercontractility at the molecular level.

    View details for DOI 10.1038/s41467-019-10555-9

    View details for PubMedID 31213605

  • Controlling load-dependent kinetics of beta-cardiac myosin at the single-molecule level. Nature structural & molecular biology Liu, C., Kawana, M., Song, D., Ruppel, K. M., Spudich, J. A. 2018; 25 (6): 505–14


    Concepts in molecular tension sensing in biology are growing and have their origins in studies of muscle contraction. In the heart muscle, a key parameter of contractility is the detachment rate of myosin from actin, which determines the time that myosin is bound to actin in a force-producing state and, importantly, depends on the load (force) against which myosin works. Here we measure the detachment rate of single molecules of human beta-cardiac myosin and its load dependence. We find that both can be modulated by both small-molecule compounds and cardiomyopathy-causing mutations. Furthermore, effects of mutations can be reversed by introducing appropriate compounds. Our results suggest that activating versus inhibitory perturbations of cardiac myosin are discriminated by the aggregate result on duty ratio, average force, and ultimately average power output and suggest that cardiac contractility can be controlled by tuning the load-dependent kinetics of single myosin molecules.

    View details for PubMedID 29867217

  • SETD3 is an actin histidine methyltransferase that prevents primary dystocia. Nature Wilkinson, A. W., Diep, J., Dai, S., Liu, S., Ooi, Y. S., Song, D., Li, T. M., Horton, J. R., Zhang, X., Liu, C., Trivedi, D. V., Ruppel, K. M., Vilches-Moure, J. G., Casey, K. M., Mak, J., Cowan, T., Elias, J. E., Nagamine, C. M., Spudich, J. A., Cheng, X., Carette, J. E., Gozani, O. 2018


    For more than 50 years, the methylation of mammalian actin at histidine 73 has been known to occur1. Despite the pervasiveness of His73 methylation, which we find is conserved in several model animals and plants, its function remains unclear and the enzyme that generates this modification is unknown. Here we identify SET domain protein 3 (SETD3) as the physiological actin His73 methyltransferase. Structural studies reveal that an extensive network of interactions clamps the actin peptide onto the surface of SETD3 to orient His73 correctly within the catalytic pocket and to facilitate methyl transfer. His73 methylation reduces the nucleotide-exchange rate on actin monomers and modestly accelerates the assembly of actin filaments. Mice that lack SETD3 show complete loss of actin His73 methylation in several tissues, and quantitative proteomics analysis shows that actin His73 methylation is the only detectable physiological substrate of SETD3. SETD3-deficient female mice have severely decreased litter sizes owing to primary maternal dystocia that is refractory to ecbolic induction agents. Furthermore, depletion of SETD3 impairs signal-induced contraction in primary human uterine smooth muscle cells. Together, our results identify a mammalian histidine methyltransferase and uncover a pivotal role for SETD3 and actin His73 methylation in the regulation of smooth muscle contractility. Our data also support the broader hypothesis that protein histidine methylation acts as a common regulatory mechanism.

    View details for PubMedID 30626964

  • A network of cis and trans interactions is required for ParB spreading. Nucleic acids research Song, D., Rodrigues, K., Graham, T. G., Loparo, J. J. 2017


    Most bacteria utilize the highly conserved parABS partitioning system in plasmid and chromosome segregation. This system depends on a DNA-binding protein ParB, which binds specifically to the centromere DNA sequence parS and to adjacent non-specific DNA over multiple kilobases in a phenomenon called spreading. Previous single-molecule experiments in combination with genetic, biochemical and computational studies have argued that ParB spreading requires cooperative interactions between ParB dimers including DNA bridging and possible nearest-neighbor interactions. A recent structure of a ParB homolog co-crystallized with parS revealed that ParB dimers tetramerize to form a higher order nucleoprotein complex. Using this structure as a guide, we systematically ablated a series of proposed intermolecular interactions in the Bacillus subtilis ParB (BsSpo0J) and characterized their effect on spreading using both in vivo and in vitro assays. In particular, we measured DNA compaction mediated by BsSpo0J using a recently developed single-molecule method to simultaneously visualize protein binding on single DNA molecules and changes in DNA conformation without protein labeling. Our results indicate that residues acting as hubs for multiple interactions frequently led to the most severe spreading defects when mutated, and that a network of both cis and trans interactions between ParB dimers is necessary for spreading.

    View details for DOI 10.1093/nar/gkx271

    View details for PubMedID 28407103

  • A general approach to visualize protein binding and DNA conformation without protein labelling NATURE COMMUNICATIONS Song, D., Graham, T. G., Loparo, J. J. 2016; 7


    Single-molecule manipulation methods, such as magnetic tweezers and flow stretching, generally use the measurement of changes in DNA extension as a proxy for examining interactions between a DNA-binding protein and its substrate. These approaches are unable to directly measure protein-DNA association without fluorescently labelling the protein, which can be challenging. Here we address this limitation by developing a new approach that visualizes unlabelled protein binding on DNA with changes in DNA conformation in a relatively high-throughput manner. Protein binding to DNA molecules sparsely labelled with Cy3 results in an increase in fluorescence intensity due to protein-induced fluorescence enhancement (PIFE), whereas DNA length is monitored under flow of buffer through a microfluidic flow cell. Given that our assay uses unlabelled protein, it is not limited to the low protein concentrations normally required for single-molecule fluorescence imaging and should be broadly applicable to studying protein-DNA interactions.

    View details for DOI 10.1038/ncomms10976

    View details for Web of Science ID 000371726100001

    View details for PubMedID 26952553

  • DNA Motion Capture Reveals the Mechanical Properties of DNA at the Mesoscale BIOPHYSICAL JOURNAL Price, A. C., Pilkiewicz, K. R., Graham, T. G., Song, D., Eaves, J. D., Loparo, J. J. 2015; 108 (10): 2532-2540


    Single-molecule studies probing the end-to-end extension of long DNAs have established that the mechanical properties of DNA are well described by a wormlike chain force law, a polymer model where persistence length is the only adjustable parameter. We present a DNA motion-capture technique in which DNA molecules are labeled with fluorescent quantum dots at specific sites along the DNA contour and their positions are imaged. Tracking these positions in time allows us to characterize how segments within a long DNA are extended by flow and how fluctuations within the molecule are correlated. Utilizing a linear response theory of small fluctuations, we extract elastic forces for the different, ∼2-μm-long segments along the DNA backbone. We find that the average force-extension behavior of the segments can be well described by a wormlike chain force law with an anomalously small persistence length.

    View details for DOI 10.1016/j.bpj.2015.04.022

    View details for Web of Science ID 000354827200013

    View details for PubMedID 25992731

  • Tethered particle motion with single DNA molecules AMERICAN JOURNAL OF PHYSICS Song, D., Mousley, B., Gambino, S., Helou, E., Loparo, J., Price, A. C. 2015; 83 (5): 418-426

    View details for DOI 10.1119/1.4902187

    View details for Web of Science ID 000353306500005

  • Building bridges within the bacterial chromosome TRENDS IN GENETICS Song, D., Loparo, J. J. 2015; 31 (3): 164-173


    All organisms must dramatically compact their genomes to accommodate DNA within the cell. Bacteria use a set of DNA-binding proteins with low sequence specificity called nucleoid-associated proteins (NAPs) to assist in chromosome condensation and organization. By bending or bridging DNA, NAPs also facilitate chromosome segregation and regulate gene expression. Over the past decade, emerging single-molecule and chromosome conformation capture techniques have investigated the molecular mechanisms by which NAPs remodel and organize the bacterial chromosome. In this review we describe how such approaches reveal the biochemical mechanisms of three NAPs that are believed to facilitate DNA bridging: histone-like nucleoid structuring protein (H-NS), ParB, and structural maintenance of chromosomes (SMC). These three proteins form qualitatively different DNA bridges, leading to varied effects on transcription and chromosome segregation.

    View details for DOI 10.1016/j.tig.2015.01.003

    View details for Web of Science ID 000350932300007

    View details for PubMedID 25682183

  • ParB spreading requires DNA bridging GENES & DEVELOPMENT Graham, T. G., Wang, X., Song, D., Etson, C. M., van Oijen, A. M., Rudner, D. Z., Loparo, J. J. 2014; 28 (11): 1228-1238


    The parABS system is a widely employed mechanism for plasmid partitioning and chromosome segregation in bacteria. ParB binds to parS sites on plasmids and chromosomes and associates with broad regions of adjacent DNA, a phenomenon known as spreading. Although essential for ParB function, the mechanism of spreading remains poorly understood. Using single-molecule approaches, we discovered that Bacillus subtilis ParB (Spo0J) is able to trap DNA loops. Point mutants in Spo0J that disrupt DNA bridging are defective in spreading and recruitment of structural maintenance of chromosomes (SMC) condensin complexes in vivo. DNA bridging helps to explain how a limited number of Spo0J molecules per parS site (~20) can spread over many kilobases and suggests a mechanism by which ParB proteins could facilitate the loading of SMC complexes. We show that DNA bridging is a property of diverse ParB homologs, suggesting broad evolutionary conservation.

    View details for DOI 10.1101/gad.242206.114

    View details for Web of Science ID 000337210600010

    View details for PubMedID 24829297

  • The Transcription Factor Titration Effect Dictates Level of Gene Expression CELL Brewster, R. C., Weinert, F. M., Garcia, H. G., Song, D., Rydenfelt, M., Phillips, R. 2014; 156 (6): 1312-1323


    Models of transcription are often built around a picture of RNA polymerase and transcription factors (TFs) acting on a single copy of a promoter. However, most TFs are shared between multiple genes with varying binding affinities. Beyond that, genes often exist at high copy number-in multiple identical copies on the chromosome or on plasmids or viral vectors with copy numbers in the hundreds. Using a thermodynamic model, we characterize the interplay between TF copy number and the demand for that TF. We demonstrate the parameter-free predictive power of this model as a function of the copy number of the TF and the number and affinities of the available specific binding sites; such predictive control is important for the understanding of transcription and the desire to quantitatively design the output of genetic circuits. Finally, we use these experiments to dynamically measure plasmid copy number through the cell cycle.

    View details for DOI 10.1016/j.cell.2014.02.022

    View details for Web of Science ID 000332945100019

    View details for PubMedID 24612990