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Structural role for DNA Ligase IV in promoting the fidelity of non-homologous end joining
Benjamin M. Stinson, Sean M. Carney, Johannes C. Walter, Joseph J. Loparo
bioRxiv 2022 doi:
Allosteric activation of cell wall synthesis during bacterial growth
Irina Shlosman, Elayne M. Fivenson, Morgan S.A. Gilman, Tyler A. Sisley, Suzanne Walker, Thomas G. Bernhardt, Andrew C. Kruse*, Joseph J. Loparo*
bioRxiv 2022 doi:
*co-corresponding authors

Peer Reviewed Publications

Replication stalling activates SSB for recruitment of DNA damage tolerance factors
Thrall, E.S.*, Piatt, S.C.*, Chang, S., Loparo, J.J.
PNAS 119 (2022) e2208875119
H2A.Z deposition by SWR1C involves multiple ATP-dependent steps
Fan, J.*, Moreno, A.T.*, Baier, A.S., Loparo, J.J.**, Peterson, C.L.**
Nat Commun. 2022, doi: 10.1038/s41467-022-34861-x
* co-first authors, ** co-corresponding authors
Compartmentalization of the replication fork by single-stranded DNA binding protein regulates translesion synthesis
Chang, S.; Thrall, E.S.; Laureti, L.; Piatt, S.C., Pages, V.; Loparo, J.J.
NSMB 29 (2022) 932-941.

Read a perspective on this work written by Julian Sale
Repair of DNA double-strand breaks by the nonhomologous end joining pathway.
Stinson, B.M. and Loparo, J.J.
Annu Rev Biochem 2021 doi:10.1146/annurev-biochem-080320-110356
Real-time imaging of polioviral RNA translocation across a membrane
Karunatilaka, K.S.; Filman, D.J.; Strauss, M.; Loparo, J.J.; Hogle, J.M.
mBio (2021) 12(1):e03695-20. doi: 10.1128/mBio.03695-20
XLF acts as a flexible connector during non-homologous end joining
Carney, S.M.; Moreno, A.T.; Piatt, S.C.; Cisneros-Aguirre, M.; Wednesday Lopezcolorado, F.; Stark, J.M.; Loparo, J.J.
eLife 9 (2020) e61920 doi: 10.7554/eLife.61920
Self-efficacy and performance of research skills among first-semester bioscience doctoral students
Lachance, K.; Heustis, R.J.; Loparo, J.J.; Venkatesh, M.V.
CBE Life Sci. Educ. (2020) doi:10.1187/cbe.19-07-0142
Catalytically inactive T7 DNA polymerase imposes a lethal replication roadblock
Hernandez, A.J.; Lee, S.J.; Chang, S.; Lee, J.A.; Loparo, J.J.; Richardson, C.C.
J. Biol. Chem. (2020) doi: 10.1074/jbc.RA120.013738.
A mechanism to minimize errors during non-homologous end joining.
Stinson, B.M.; Moreno, A.T.; Walter, J.C.; Loparo, J.J.
Mol Cell (2019)
Embedding academic and professional skills training with experimental-design chalk talks.
Heustis, R.J.; Venkatesh, M.J.; Gutlerner, J.L.; Loparo, J.J.
Nat. Biotechnol. 37 (2019) 1523-1527.
A gatekeeping function of the replicative polymerase controls pathway choice in the resolution of lesion-stalled replisomes.
Chang, S.; Naiman, K.; Thrall, E.S.; Kath, J.E.; Jergic, S.; Dixon, N.E.; Fuchs, R.P.; Loparo, J.J.
Proc. Natl. Acad. Sci. USA 116 (2019) 25591-25601.
The gene silencing protein MORC-1 topologically entraps DNA and forms multimeric assemblies to cause DNA compaction.
Kim, H; Yen, L; Wongpalee, S.p.; Kirshner, J.A.; Mehta, N.; Xue, Y, Johnston, J.B.; Burlingame, A.L.; Kim, J.K.; Loparo, J.J.*; Jacobsen, S.E.*
Mol Cell 75 (2019) 700-710. *Co-corresponding authors
The role of noncognant sites in the EcoRI search mechanism.
Piatt, S.C.; Loparo, J.J.*; Price, A.C.*
Biophys J 116 (2019) 2367-2377. *Co-corresponding authors
A Flow-extension tethered particle motion assay for single-molecule proteolysis.
Drabek, A.A.; Loparo, J.J.*; Blacklow, S.C.*
Biochemistry 58 (2019) 2509-2518. *Co-corresponding authors
Protein translocation by the SecA ATPase occurs by a power-stroke mechanism.
Catipovic, M.A.; Bauer, B.W.; Loparo, J.J.; Rapoport, T.A.
EMBO J 38 (2019) e101140.
A single XLF dimer bridges DNA ends during non-homologous end joining.
Graham, T.G.W.*; Carney, S.M.*; Walter, J.C.; Loparo, J.J.
Nat. Struct. Mol. Biol. 25 (2018) 877-884.
Single-molecule imaging reveals multiple pathway for the recruitment of translesion polymerases after
DNA damage. Thrall, E.S.; Kath, J.E.; Chang, S.; Loparo, J.J.;
Nat. Commun. (2017) doi: 10.1038/s41467-017-02333-2.
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.
Recommended by Faculty of 1000
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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