Publications

Independent Career @ HMS

  • Ensemble and single-molecule analysis of non-homologous end joining in frog egg extracts. Graham, T.G.W.; Walter J.C.; Loparo, J.J.; Methods Enzymol 591 (2017) 233-270.
  • A network of cis and trans interactions is required for ParB spreading. Song, D.; Rodrigues, K.; Graham, T.G.W.; Loparo, J.J.; Nucleic Acids Res. (2017) doi: 10.1093/nar/gkx271.
    Recommended by Faculty of 1000
  • Mapping DNA polymerase errors by single-molecule sequencing. Lee, D.F.; Lu, J.; Chang, S.; Loparo, J.J.; Xie, X.S. Nucleic Acids Res 44 (2016) e118.
  • Two-stage synapsis of DNA ends during non-homologous end joining. Graham, T.G.W.; Walter, J.C.; Loparo, J.J. Mol Cell 61 (2016) 850-8.
  • A general approach to visualize protein binding and DNA conformation without protein labeling. Song, D.; Graham, T.G.W.; Loparo, J.J. Nat. Commun. (2016) doi: 10.1038/ncomms10976.
  • A single molecule assay for measuring site specific DNA cleavage. Gambino, S.; Mousley, B.; Cathcart, L.; Winship, J.; Loparo, J.J.; Price, A.C.; Analytical Biochem (2015) doi:10. 1016/j.ab.2015.11.013.
  • Exchange between Escherichia coli Polymerases II and III on a processivity clamp. Kath, J.E.; Chang, S.; Scotland, M.K.; Wilbertz, J.H.; Jergic, S.; Dixon, N.E.; Sutton, M.D.; Loparo, J.J.; Nucleic Acids Res (2015) doi:10.1093/nar/gkv1375.
  • Multistep assembly of DNA condensation clusters by SMC. Kim, H.; Loparo, J.J.; Nat. Commun. (2016) doi: 10.1038/ncomms10200.
  • A genetic selection for dinB mutants reveals an interaction between DNA Polymerase IV and the replicative polymerase that is required for translesion synthesis. Scotland, M.K.; Heltzel, J.M.H.; Kath, J.E.; Choi, J-S; Berdis, A.J.; Loparo, J.J.; Sutton, M.D.; PLOS Genetics 11 (2015) e1005507.
  • Mechanical allostery: Evidence for a force requirement in the proteolytic activation of Notch. Gordon, W.R.; Zimmerman B.; He, L.; Miles, L.J.; Huang, J.; Tiyanont, K.; McArthur, D.G.; Aster, J.C.; Perrimon, N.; Loparo, J.J.*; Blacklow, S.C.* Dev Cell 33 (2015) 729-736.
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  • DNA motion capture reveals the mechanical properties of DNA at the mesoscale. Price, A.C.; Pilkiewicz, K.R.; Graham, T.G.W.; Song, Dan; Eaves, J.D.; Loparo, J.J. Biophys J. 108 (2015) 2532-2540.
  • Building bridges within the bacterial chromosome. Song, D. and Loparo, JJ. Trends Genet 31 (2015) 164-173.
  • Tethered particle motion with single DNA molecules. Song, D.; Mousley, B.; Gambino, S.; Helou, E.; Loparo, J.J.; Price, A.C. Am. J. Phys. 83 (2015) 418-426.
  • Condensation and localization of the partitioning protein ParB on the bacterial chromosome. Broedersz C.P.; Wang, X.; Meir, Y.; Loparo, J.J.; Rudner, D.Z.; Wingreen, N.S. Proc. Natl. Acad. Sci. USA 111 (2014) 8809-14.
  • ParB spreading requires DNA bridging. Graham, T.G.W.; Wang, X.; Song, D.; Etson, C.M.; van Oijen, A.M.; Rudner, D.Z.; Loparo, J.J. Genes Dev 28 (2014) 1228-38.
    Read a perspective on this work written by Barbara Funnell
  • Polymerase exchange on single DNA molecules reveals processivity clamp control of translesion synthesis. Kath, J.E,; Jergic, S.; Heltzel, J.M.H.; Jacob, D.T.; Dixon, N.E.; Sutton, M.D.; Walker, G.C.; Loparo, J.J. Proc. Natl. Acad. Sci. USA 111 (2014) 7647-52.
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Postdoctoral Research

  • E. coli DNA replication in the absence of free β clamps Tanner, N.A.; Tolun, G.; Loparo, J.J.; Jergic, S.; Griffith, J.D.; Dixon, N.E.; van Oijen, A.M. EMBO J. (2011, ahead of print)
  • Observing polymerase exchange by simultaneous measurements of replisome composition and function at the single-molecule level. Loparo, J.J.; Kukczyk, A.W.; Richardson, C.C.; van Oijen, A.M.; PNAS, 108, (2011) 3584-3589.
  • Single-molecule studies of the replisome. van Oijen, A.M. and Loparo, J.J. Ann. Rev. Biophys 39 (2010) 429-48.
  • The PCNA sliding clamp uses two distinct sliding modes to move along DNA. Kochaniak, A.B.; Habuchi, S.; Loparo, J.J.; Chang, D.J.; Cimprich, K.A.; Walter, J.C.; van Oijen, A.M.; J. Biol. Chem. 284 (2009) 17700-10.
  • Real-time single-molecule observation of rolling-circle DNA replication. Tanner, N.A*.; Loparo, J.J.*; Hamdan, S.M.; Jergic, S.; Dixon, N.E.; van Oijen, A.M.; Nucleic Acids Res. 37 (2009) e27. *equal contribution
  • Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis. Hamdan, S.M.; Loparo, J.J.; Takahashi, M.; Richardson, C.C.; van Oijen, A.M.; Nature 457 (2009) 336-9.