Honors & Awards

  • Beckman Postdoctoral Fellowship (Independence award; mentored phase), Arnold and Mabel Beckman Foundation (2017-present)
  • Stanford Medicine Dean's Postdoctoral Fellowship, Stanford (2016-2017)

Professional Education

  • Bachelor of Science, University of Texas at Dallas, Molecular Cell Biology and Biophysics (2008)
  • Master of Science, University of Texas at Dallas, Molecular and Cell Biology (2010)
  • Doctor of Philosophy, University of Texas at Dallas, Molecular and Cell Biology (2013)
  • Doctor of Philosophy, University of Texas at Dallas, Biomedical Engineering (2015)

Stanford Advisors

All Publications

  • Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens G3: GENES, GENOMES, GENETICS Shoura, M., Gabdank, I., Merker, J., Gotlib, J., Levene, S., Fire, A. 2017; 7: 3295-3303


    Investigations aimed at defining the 3D configuration of eukaryotic chromosomes have consistently encountered an endogenous population of chromosome-derived circular genomic DNA, referred to as extrachromosomal circular DNA (eccDNA). While the production, distribution, and activities of eccDNAs remain understudied, eccDNA formation from specific regions of the linear genome has profound consequences on the regulatory and coding capabilities for these regions. Here, we define eccDNA distributions in Caenorhabditis elegans and in three human cell types, utilizing a set of DNA topology-dependent approaches for enrichment and characterization. The use of parallel biophysical, enzymatic, and informatic approaches provides a comprehensive profiling of eccDNA robust to isolation and analysis methodology. Results in human and nematode systems provide quantitative analysis of the eccDNA loci at both unique and repetitive regions. Our studies converge on and support a consistent picture, in which endogenous genomic DNA circles are present in normal physiological states, and in which the circles come from both coding and noncoding genomic regions. Prominent among the coding regions generating DNA circles are several genes known to produce a diversity of protein isoforms, with mucin proteins and titin as specific examples.

    View details for DOI 10.1534/g3.117.300141

    View details for PubMedCentralID PMC5633380

  • Contribution of Fluorophore Dynamics and Solvation to Resonant Energy Transfer in Protein-DNA Complexes: A Molecular-Dynamics Study BIOPHYSICAL JOURNAL Shoura, M. J., Ranatunga, R. J., Harris, S. A., Nielsen, S. O., Levene, S. D. 2014; 107 (3): 700-710


    In Förster resonance energy transfer (FRET) experiments, extracting accurate structural information about macromolecules depends on knowing the positions and orientations of donor and acceptor fluorophores. Several approaches have been employed to reduce uncertainties in quantitative FRET distance measurements. Fluorophore-position distributions can be estimated by surface accessibility (SA) calculations, which compute the region of space explored by the fluorophore within a static macromolecular structure. However, SA models generally do not take fluorophore shape, dye transition-moment orientation, or dye-specific chemical interactions into account. We present a detailed molecular-dynamics (MD) treatment of fluorophore dynamics for an ATTO donor/acceptor dye pair and specifically consider as case studies dye-labeled protein-DNA intermediates in Cre site-specific recombination. We carried out MD simulations in both an aqueous solution and glycerol/water mixtures to assess the effects of experimental solvent systems on dye dynamics. Our results unequivocally show that MD simulations capture solvent effects and dye-dye interactions that can dramatically affect energy transfer efficiency. We also show that results from SA models and MD simulations strongly diverge in cases where donor and acceptor fluorophores are in close proximity. Although atomistic simulations are computationally more expensive than SA models, explicit MD studies are likely to give more realistic results in both homogeneous and mixed solvents. Our study underscores the model-dependent nature of FRET analyses, but also provides a starting point to develop more realistic in silico approaches for obtaining experimental ensemble and single-molecule FRET data.

    View details for DOI 10.1016/j.bpj.2014.06.023

    View details for Web of Science ID 000340018000020

    View details for PubMedID 25099809

  • Measurements of DNA-loop formation via Cre-mediated recombination NUCLEIC ACIDS RESEARCH Shoura, M. J., Vetcher, A. A., Giovan, S. M., Bardai, F., Bharadwaj, A., Kesinger, M. R., Levene, S. D. 2012; 40 (15): 7452-7464


    The Cre-recombination system has become an important tool for genetic manipulation of higher organisms and a model for site-specific DNA-recombination mechanisms employed by the λ-Int superfamily of recombinases. We report a novel quantitative approach for characterizing the probability of DNA-loop formation in solution using time-dependent ensemble Förster resonance energy transfer measurements of intra- and inter-molecular Cre-recombination kinetics. Our method uses an innovative technique for incorporating multiple covalent modifications at specific sites in covalently closed DNA. Because the mechanism of Cre recombinase does not conform to a simple kinetic scheme, we employ numerical methods to extract rate constants for fundamental steps that pertain to Cre-mediated loop closure. Cre recombination does not require accessory proteins, DNA supercoiling or particular metal-ion cofactors and is thus a highly flexible system for quantitatively analyzing DNA-loop formation in vitro and in vivo.

    View details for DOI 10.1093/nar/gks430

    View details for Web of Science ID 000308958600044

    View details for PubMedID 22589415

  • Circulomics: The Structural Genomics of Endogenous and Exogenous Extrachromosomal Circular DNAs Levene, S. D., Shoura, M. J., Fire, A. Z. CELL PRESS. 2018: 83A
  • Circulomics: Ultrasensitive Characterization of Extrachromosomal Circular DNA (eccDNA) Distributions and Functions in Eukaryotes Shoura, M., Levene, S., Fire, A. CELL PRESS. 2018: 83A
  • Quantitative Characterization of Gel Electrophoresis Images Ziraldo, R., Shoura, M. J., Leven, S. D. CELL PRESS. 2018: 540A
  • The thermodynamics of DNA loop formation, from J to Z BIOCHEMICAL SOCIETY TRANSACTIONS Levene, S. D., Giovan, S. M., Hanke, A., Shoura, M. J. 2013; 41: 513-518


    The formation of DNA loops is a ubiquitous theme in biological processes, including DNA replication, recombination and repair, and gene regulation. These loops are mediated by proteins bound at specific sites along the contour of a single DNA molecule, in some cases many thousands of base pairs apart. Loop formation incurs a thermodynamic cost that is a sensitive function of the length of looped DNA as well as the geometry and elastic properties of the DNA-bound protein. The free energy of DNA looping is logarithmically related to a generalization of the Jacobson-Stockmayer factor for DNA cyclization, termed the J factor. In the present article, we review the thermodynamic origins of this quantity, discuss how it is measured experimentally and connect the macroscopic interpretation of the J factor with a statistical-mechanical description of DNA looping and cyclization.

    View details for DOI 10.1042/BST20120324

    View details for Web of Science ID 000316560900007

    View details for PubMedID 23514145

  • Understanding DNA looping through Cre-recombination kinetics Discrete and Topological Models in Molecular Biology Shoura, M., Levene, S. 2013