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Items: 36


The Role of Noncognate Sites in the 1D Search Mechanism of EcoRI.

Piatt SC, Loparo JJ, Price AC.

Biophys J. 2019 Jun 18;116(12):2367-2377. doi: 10.1016/j.bpj.2019.04.035. Epub 2019 May 8.


A Flow-Extension Tethered Particle Motion Assay for Single-Molecule Proteolysis.

Drabek AA, Loparo JJ, Blacklow SC.

Biochemistry. 2019 May 21;58(20):2509-2518. doi: 10.1021/acs.biochem.9b00106. Epub 2019 Apr 12.


Protein translocation by the SecA ATPase occurs by a power-stroke mechanism.

Catipovic MA, Bauer BW, Loparo JJ, Rapoport TA.

EMBO J. 2019 May 2;38(9). pii: e101140. doi: 10.15252/embj.2018101140. Epub 2019 Mar 15.


Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes.

Klein HL, Ang KKH, Arkin MR, Beckwitt EC, Chang YH, Fan J, Kwon Y, Morten MJ, Mukherjee S, Pambos OJ, El Sayyed H, Thrall ES, Vieira-da-Rocha JP, Wang Q, Wang S, Yeh HY, Biteen JS, Chi P, Heyer WD, Kapanidis AN, Loparo JJ, Strick TR, Sung P, Van Houten B, Niu H, Rothenberg E.

Microb Cell. 2019 Jan 7;6(1):65-101. doi: 10.15698/mic2019.01.665. Review.


A single XLF dimer bridges DNA ends during nonhomologous end joining.

Graham TGW, Carney SM, Walter JC, Loparo JJ.

Nat Struct Mol Biol. 2018 Sep;25(9):877-884. doi: 10.1038/s41594-018-0120-y. Epub 2018 Sep 3.


Observing Bacterial Chromatin Protein-DNA Interactions by Combining DNA Flow-Stretching with Single-Molecule Imaging.

Kim H, Loparo JJ.

Methods Mol Biol. 2018;1837:277-299. doi: 10.1007/978-1-4939-8675-0_15.


Single-molecule imaging reveals multiple pathways for the recruitment of translesion polymerases after DNA damage.

Thrall ES, Kath JE, Chang S, Loparo JJ.

Nat Commun. 2017 Dec 18;8(1):2170. doi: 10.1038/s41467-017-02333-2.


Ensemble and Single-Molecule Analysis of Non-Homologous End Joining in Frog Egg Extracts.

Graham TGW, Walter JC, Loparo JJ.

Methods Enzymol. 2017;591:233-270. doi: 10.1016/bs.mie.2017.03.020. Epub 2017 May 15.


A network of cis and trans interactions is required for ParB spreading.

Song D, Rodrigues K, Graham TGW, Loparo JJ.

Nucleic Acids Res. 2017 Jul 7;45(12):7106-7117. doi: 10.1093/nar/gkx271.


Mapping DNA polymerase errors by single-molecule sequencing.

Lee DF, Lu J, Chang S, Loparo JJ, Xie XS.

Nucleic Acids Res. 2016 Jul 27;44(13):e118. doi: 10.1093/nar/gkw436. Epub 2016 May 16.


Two-Stage Synapsis of DNA Ends during Non-homologous End Joining.

Graham TG, Walter JC, Loparo JJ.

Mol Cell. 2016 Mar 17;61(6):850-8. doi: 10.1016/j.molcel.2016.02.010.


A general approach to visualize protein binding and DNA conformation without protein labelling.

Song D, Graham TG, Loparo JJ.

Nat Commun. 2016 Mar 8;7:10976. doi: 10.1038/ncomms10976.


Multistep assembly of DNA condensation clusters by SMC.

Kim H, Loparo JJ.

Nat Commun. 2016 Jan 4;7:10200. doi: 10.1038/ncomms10200.


Exchange between Escherichia coli polymerases II and III on a processivity clamp.

Kath JE, Chang S, Scotland MK, Wilbertz JH, Jergic S, Dixon NE, Sutton MD, Loparo JJ.

Nucleic Acids Res. 2016 Feb 29;44(4):1681-90. doi: 10.1093/nar/gkv1375. Epub 2015 Dec 10.


A single molecule assay for measuring site-specific DNA cleavage.

Gambino S, Mousley B, Cathcart L, Winship J, Loparo JJ, Price AC.

Anal Biochem. 2016 Feb 15;495:3-5. doi: 10.1016/j.ab.2015.11.013. Epub 2015 Dec 2.


A Genetic Selection for dinB Mutants Reveals an Interaction between DNA Polymerase IV and the Replicative Polymerase That Is Required for Translesion Synthesis.

Scotland MK, Heltzel JM, Kath JE, Choi JS, Berdis AJ, Loparo JJ, Sutton MD.

PLoS Genet. 2015 Sep 9;11(9):e1005507. doi: 10.1371/journal.pgen.1005507. eCollection 2015 Sep.


Mechanical Allostery: Evidence for a Force Requirement in the Proteolytic Activation of Notch.

Gordon WR, Zimmerman B, He L, Miles LJ, Huang J, Tiyanont K, McArthur DG, Aster JC, Perrimon N, Loparo JJ, Blacklow SC.

Dev Cell. 2015 Jun 22;33(6):729-36. doi: 10.1016/j.devcel.2015.05.004. Epub 2015 Jun 4.


DNA motion capture reveals the mechanical properties of DNA at the mesoscale.

Price AC, Pilkiewicz KR, Graham TGW, Song D, Eaves JD, Loparo JJ.

Biophys J. 2015 May 19;108(10):2532-2540. doi: 10.1016/j.bpj.2015.04.022.


Building bridges within the bacterial chromosome.

Song D, Loparo JJ.

Trends Genet. 2015 Mar;31(3):164-73. doi: 10.1016/j.tig.2015.01.003. Epub 2015 Feb 11. Review.


Condensation and localization of the partitioning protein ParB on the bacterial chromosome.

Broedersz CP, Wang X, Meir Y, Loparo JJ, Rudner DZ, Wingreen NS.

Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8809-14. doi: 10.1073/pnas.1402529111. Epub 2014 Jun 3.


ParB spreading requires DNA bridging.

Graham TG, Wang X, Song D, Etson CM, van Oijen AM, Rudner DZ, Loparo JJ.

Genes Dev. 2014 Jun 1;28(11):1228-38. doi: 10.1101/gad.242206.114. Epub 2014 May 14.


Polymerase exchange on single DNA molecules reveals processivity clamp control of translesion synthesis.

Kath JE, Jergic S, Heltzel JM, Jacob DT, Dixon NE, Sutton MD, Walker GC, Loparo JJ.

Proc Natl Acad Sci U S A. 2014 May 27;111(21):7647-52. doi: 10.1073/pnas.1321076111. Epub 2014 May 13.


E. coli DNA replication in the absence of free β clamps.

Tanner NA, Tolun G, Loparo JJ, Jergic S, Griffith JD, Dixon NE, van Oijen AM.

EMBO J. 2011 May 4;30(9):1830-40. doi: 10.1038/emboj.2011.84. Epub 2011 Mar 25.


Simultaneous single-molecule measurements of phage T7 replisome composition and function reveal the mechanism of polymerase exchange.

Loparo JJ, Kulczyk AW, Richardson CC, van Oijen AM.

Proc Natl Acad Sci U S A. 2011 Mar 1;108(9):3584-9. doi: 10.1073/pnas.1018824108. Epub 2011 Jan 18.


Single-molecule studies of the replisome.

van Oijen AM, Loparo JJ.

Annu Rev Biophys. 2010;39:429-48. doi: 10.1146/annurev.biophys.093008.131327. Review.


Direct observation of enzymes replicating DNA using a single-molecule DNA stretching assay.

Kulczyk AW, Tanner NA, Loparo JJ, Richardson CC, van Oijen AM.

J Vis Exp. 2010 Mar 23;(37). pii: 1689. doi: 10.3791/1689.


Visualizing Single-molecule DNA Replication with Fluorescence Microscopy.

Tanner NA, Loparo JJ, van Oijen AM.

J Vis Exp. 2009 Oct 9;(32). pii: 1529. doi: 10.3791/1529.


Proliferating cell nuclear antigen uses two distinct modes to move along DNA.

Kochaniak AB, Habuchi S, Loparo JJ, Chang DJ, Cimprich KA, Walter JC, van Oijen AM.

J Biol Chem. 2009 Jun 26;284(26):17700-10. doi: 10.1074/jbc.M109.008706. Epub 2009 May 3.


Real-time single-molecule observation of rolling-circle DNA replication.

Tanner NA, Loparo JJ, Hamdan SM, Jergic S, Dixon NE, van Oijen AM.

Nucleic Acids Res. 2009 Mar;37(4):e27. doi: 10.1093/nar/gkp006. Epub 2009 Jan 20.


Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis.

Hamdan SM, Loparo JJ, Takahashi M, Richardson CC, van Oijen AM.

Nature. 2009 Jan 15;457(7227):336-9. doi: 10.1038/nature07512. Epub 2008 Nov 23.


Multidimensional infrared spectroscopy of water. II. Hydrogen bond switching dynamics.

Loparo JJ, Roberts ST, Tokmakoff A.

J Chem Phys. 2006 Nov 21;125(19):194522.


Multidimensional infrared spectroscopy of water. I. Vibrational dynamics in two-dimensional IR line shapes.

Loparo JJ, Roberts ST, Tokmakoff A.

J Chem Phys. 2006 Nov 21;125(19):194521.


Characterization of spectral diffusion from two-dimensional line shapes.

Roberts ST, Loparo JJ, Tokmakoff A.

J Chem Phys. 2006 Aug 28;125(8):084502.


Hydrogen bonds in liquid water are broken only fleetingly.

Eaves JD, Loparo JJ, Fecko CJ, Roberts ST, Tokmakoff A, Geissler PL.

Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13019-22. Epub 2005 Aug 31.


Local hydrogen bonding dynamics and collective reorganization in water: ultrafast infrared spectroscopy of HOD/D(2)O.

Fecko CJ, Loparo JJ, Roberts ST, Tokmakoff A.

J Chem Phys. 2005 Feb 1;122(5):54506.


Ultrafast hydrogen-bond dynamics in the infrared spectroscopy of water.

Fecko CJ, Eaves JD, Loparo JJ, Tokmakoff A, Geissler PL.

Science. 2003 Sep 19;301(5640):1698-702.

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