☰

cached image

Joseph J. Loparo - Publications

Affiliations: 
Biological Chemistry and Molecular Pharmacology Harvard Medical School, Boston, MA, United States 
Area:
optical spectroscopy to probe the dynamics of molecules
Website:
http://www.fas.harvard.edu/~biophys/Joseph_Loparo.htm
Tree Info Similar researchers PubMed Report error

57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Hernandez AJ, Lee SJ, Chang S, Lee JA, Loparo JJ, Richardson CC. Catalytically inactive T7 DNA polymerase imposes a lethal replication roadblock. The Journal of Biological Chemistry. PMID 32430399 DOI: 10.1074/Jbc.Ra120.013738  0.323
2019 Stinson BM, Moreno AT, Walter JC, Loparo JJ. A Mechanism to Minimize Errors during Non-homologous End Joining. Molecular Cell. PMID 31862156 DOI: 10.1016/J.Molcel.2019.11.018  0.4
2019 Chang S, Naiman K, Thrall ES, Kath JE, Jergic S, Dixon NE, Fuchs RP, Loparo JJ. A gatekeeping function of the replicative polymerase controls pathway choice in the resolution of lesion-stalled replisomes. Proceedings of the National Academy of Sciences of the United States of America. PMID 31796591 DOI: 10.1073/Pnas.1914485116  0.318
2019 Kim H, Yen L, Wongpalee SP, Kirshner JA, Mehta N, Xue Y, Johnston JB, Burlingame AL, Kim JK, Loparo JJ, Jacobsen SE. The Gene-Silencing Protein MORC-1 Topologically Entraps DNA and Forms Multimeric Assemblies to Cause DNA Compaction. Molecular Cell. 75: 700-710.e6. PMID 31442422 DOI: 10.1016/J.Molcel.2019.07.032  0.399
2019 Piatt SC, Loparo JJ, Price AC. The Role of Noncognate Sites in the 1D Search Mechanism of EcoRI. Biophysical Journal. PMID 31113551 DOI: 10.1016/j.bpj.2019.04.035  0.326
2019 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, ... ... Loparo JJ, et al. Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes. Microbial Cell (Graz, Austria). 6: 65-101. PMID 30652106 DOI: 10.15698/Mic2019.01.665  0.363
2019 Kim H, Yen L, Wongpalee S, Loparo J, Jacobsen S. Caenorhabditis elegans MORC-1 Topologically Traps and Compacts DNA Biophysical Journal. 116: 502a. DOI: 10.1016/J.Bpj.2018.11.2709  0.362
2018 Graham TGW, Carney SM, Walter JC, Loparo JJ. A single XLF dimer bridges DNA ends during nonhomologous end joining. Nature Structural & Molecular Biology. 25: 877-884. PMID 30177755 DOI: 10.1038/S41594-018-0120-Y  0.375
2018 Kim H, Loparo JJ. Observing Bacterial Chromatin Protein-DNA Interactions by Combining DNA Flow-Stretching with Single-Molecule Imaging. Methods in Molecular Biology (Clifton, N.J.). 1837: 277-299. PMID 30109616 DOI: 10.1007/978-1-4939-8675-0_15  0.407
2017 Thrall ES, Kath JE, Chang S, Loparo JJ. Single-molecule imaging reveals multiple pathways for the recruitment of translesion polymerases after DNA damage. Nature Communications. 8: 2170. PMID 29255195 DOI: 10.1038/S41467-017-02333-2  0.381
2017 Graham TGW, Walter JC, Loparo JJ. Ensemble and Single-Molecule Analysis of Non-Homologous End Joining in Frog Egg Extracts. Methods in Enzymology. 591: 233-270. PMID 28645371 DOI: 10.1016/Bs.Mie.2017.03.020  0.406
2017 Song D, Rodrigues K, Graham TG, Loparo JJ. A network of cis and trans interactions is required for ParB spreading. Nucleic Acids Research. PMID 28407103 DOI: 10.1093/Nar/Gkx271  0.401
2016 Lee DF, Lu J, Chang S, Loparo JJ, Xie XS. Mapping DNA polymerase errors by single-molecule sequencing. Nucleic Acids Research. PMID 27185891 DOI: 10.1093/nar/gkw436  0.474
2016 Graham TG, Walter JC, Loparo JJ. Two-Stage Synapsis of DNA Ends during Non-homologous End Joining. Molecular Cell. 61: 850-8. PMID 26990988 DOI: 10.1016/J.Molcel.2016.02.010  0.411
2016 Song D, Graham TG, Loparo JJ. A general approach to visualize protein binding and DNA conformation without protein labelling. Nature Communications. 7: 10976. PMID 26952553 DOI: 10.1038/Ncomms10976  0.376
2016 Kim H, Loparo JJ. Multistep assembly of DNA condensation clusters by SMC. Nature Communications. 7: 10200. PMID 26725510 DOI: 10.1038/Ncomms10200  0.395
2016 Kath JE, Thrall ES, Loparo JJ. Visualizing Translesion Synthesis by Pol IV in live E. Coli Cells at Single-Molecule Resolution Biophysical Journal. 110: 65a. DOI: 10.1016/J.Bpj.2015.11.415  0.407
2016 Kim H, Loparo JJ. Visualizing the Assembly of DNA Condensation Clusters by SMC using Single-Molecule Microscopy Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.2757  0.404
2015 Kath JE, Chang S, Scotland MK, Wilbertz JH, Jergic S, Dixon NE, Sutton MD, Loparo JJ. Exchange between Escherichia coli polymerases II and III on a processivity clamp. Nucleic Acids Research. PMID 26657641 DOI: 10.1093/Nar/Gkv1375  0.341
2015 Gambino S, Mousley B, Cathcart L, Winship J, Loparo JJ, Price AC. A single molecule assay for measuring site specific DNA cleavage. Analytical Biochemistry. PMID 26655389 DOI: 10.1016/j.ab.2015.11.013  0.419
2015 Scotland MK, Heltzel JM, Kath JE, Choi JS, Berdis AJ, Loparo JJ, Sutton MD. A Genetic Selection for dinB Mutants Reveals an Interaction between DNA Polymerase IV and the Replicative Polymerase That Is Required for Translesion Synthesis. Plos Genetics. 11: e1005507. PMID 26352807 DOI: 10.1371/Journal.Pgen.1005507  0.347
2015 Price AC, Pilkiewicz KR, Graham TG, Song D, Eaves JD, Loparo JJ. DNA motion capture reveals the mechanical properties of DNA at the mesoscale. Biophysical Journal. 108: 2532-40. PMID 25992731 DOI: 10.1016/J.Bpj.2015.04.022  0.725
2015 Song D, Loparo JJ. Building bridges within the bacterial chromosome. Trends in Genetics : Tig. 31: 164-73. PMID 25682183 DOI: 10.1016/j.tig.2015.01.003  0.341
2015 Song D, Mousley B, Gambino S, Helou E, Loparo J, Price AC. Tethered particle motion with single DNA molecules American Journal of Physics. 83: 418-426. DOI: 10.1119/1.4902187  0.366
2014 Broedersz CP, Wang X, Meir Y, Loparo JJ, Rudner DZ, Wingreen NS. Condensation and localization of the partitioning protein ParB on the bacterial chromosome. Proceedings of the National Academy of Sciences of the United States of America. 111: 8809-14. PMID 24927534 DOI: 10.1073/Pnas.1402529111  0.424
2014 Graham TG, Wang X, Song D, Etson CM, van Oijen AM, Rudner DZ, Loparo JJ. ParB spreading requires DNA bridging. Genes & Development. 28: 1228-38. PMID 24829297 DOI: 10.1101/Gad.242206.114  0.782
2014 Kath JE, Jergic S, Heltzel JM, Jacob DT, Dixon NE, Sutton MD, Walker GC, Loparo JJ. Polymerase exchange on single DNA molecules reveals processivity clamp control of translesion synthesis. Proceedings of the National Academy of Sciences of the United States of America. 111: 7647-52. PMID 24825884 DOI: 10.1073/Pnas.1321076111  0.386
2014 Price AC, Mousley B, Gambino S, Helou E, Song DL, Loparo J. Measuring Kinetics of DNA Cleavage with Single Molecule Resolution Biophysical Journal. 106: 70a. DOI: 10.1016/J.BPJ.2013.11.463  0.423
2013 Graham TG, Song L, Wang X, Etson CM, Van Oijen A, Rudner DZ, Loparo JJ. Single-Molecule Studies of a ParB Family Chromosome Segregation Protein from Bacillussubtilis Biophysical Journal. 104: 582a-583a. DOI: 10.1016/J.Bpj.2012.11.3236  0.758
2013 Kim H, Loparo J. Single-Molecule Studies of Chromosome Organization by SMC Biophysical Journal. 104: 39a. DOI: 10.1016/J.Bpj.2012.11.254  0.391
2011 Tanner NA, Tolun G, Loparo JJ, Jergic S, Griffith JD, Dixon NE, van Oijen AM. E. coli DNA replication in the absence of free β clamps. The Embo Journal. 30: 1830-40. PMID 21441898 DOI: 10.1038/Emboj.2011.84  0.744
2011 Loparo JJ, Kulczyk AW, Richardson CC, van Oijen AM. Simultaneous single-molecule measurements of phage T7 replisome composition and function reveal the mechanism of polymerase exchange. Proceedings of the National Academy of Sciences of the United States of America. 108: 3584-9. PMID 21245349 DOI: 10.1073/Pnas.1018824108  0.634
2011 Williams K, Grafe B, Burke KM, Tanner N, Van Oijen AM, Loparo J, Price AC. A single molecule DNA flow stretching microscope for undergraduates American Journal of Physics. 79: 1112-1120. DOI: 10.1119/1.3620410  0.758
2011 Roberts ST, Loparo JJ, Ramasesha K, Tokmakoff A. A fast-scanning Fourier transform 2D IR interferometer Optics Communications. 284: 1062-1066. DOI: 10.1016/J.Optcom.2010.10.049  0.76
2011 Loparo JJ. Visualizing the Dynamics of DNA Polymerase Exchange Through Simultaneous Single-Molecule Measurements of Replisome Composition and Function Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.262  0.442
2010 van Oijen AM, Loparo JJ. Single-molecule studies of the replisome. Annual Review of Biophysics. 39: 429-48. PMID 20462378 DOI: 10.1146/annurev.biophys.093008.131327  0.639
2010 Kulczyk AW, Tanner NA, Loparo JJ, Richardson CC, van Oijen AM. Direct observation of enzymes replicating DNA using a single-molecule DNA stretching assay. Journal of Visualized Experiments : Jove. PMID 20332766 DOI: 10.3791/1689  0.763
2009 Tanner NA, Loparo JJ, van Oijen AM. Visualizing Single-molecule DNA Replication with Fluorescence Microscopy. Journal of Visualized Experiments : Jove. PMID 19820685 DOI: 10.3791/1529  0.76
2009 Kochaniak AB, Habuchi S, Loparo JJ, Chang DJ, Cimprich KA, Walter JC, van Oijen AM. Proliferating cell nuclear antigen uses two distinct modes to move along DNA. The Journal of Biological Chemistry. 284: 17700-10. PMID 19411704 DOI: 10.1074/Jbc.M109.008706  0.627
2009 Tanner NA, Loparo JJ, Hamdan SM, Jergic S, Dixon NE, van Oijen AM. Real-time single-molecule observation of rolling-circle DNA replication. Nucleic Acids Research. 37: e27. PMID 19155275 DOI: 10.1093/Nar/Gkp006  0.761
2009 Hamdan SM, Loparo JJ, Takahashi M, Richardson CC, van Oijen AM. Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis. Nature. 457: 336-9. PMID 19029884 DOI: 10.1016/J.Bpj.2008.12.3720  0.62
2009 Loparo JJ, Roberts ST, Nicodemus RA, Tokmakoff A. Erratum to “Variation of the transition dipole across the OH stretching band of water” [Chem. Phys. 341 (2007) 218–229] Chemical Physics. 361: 185. DOI: 10.1016/J.Chemphys.2009.06.001  0.665
2009 Loparo JJ, Hamdan SM, Richardson CC, van Antoine Oijen M. Single-molecule Observations of Replisome Structure and Function Biophysical Journal. 96: 556a-557a. DOI: 10.1016/J.Bpj.2008.12.3655  0.432
2007 Loparo JJ, Roberts ST, Nicodemus RA, Tokmakoff A. Variation of the transition dipole moment across the OH stretching band of water Chemical Physics. 341: 218-229. DOI: 10.1016/J.Chemphys.2007.06.056  0.738
2007 Schmidt JR, Roberts ST, Loparo JJ, Tokmakoff A, Fayer MD, Skinner JL. Are water simulation models consistent with steady-state and ultrafast vibrational spectroscopy experiments? Chemical Physics. 341: 143-157. DOI: 10.1016/J.Chemphys.2007.06.043  0.748
2007 Loparo JJ, Roberts ST, Tokmakoff A. 2D IR spectroscopy of hydrogen bond switching in liquid water Springer Series in Chemical Physics. 88: 341-343. DOI: 10.1007/978-3-540-68781-8-110  0.711
2006 Loparo JJ, Roberts ST, Tokmakoff A. Multidimensional infrared spectroscopy of water. II. Hydrogen bond switching dynamics. The Journal of Chemical Physics. 125: 194522. PMID 17129138 DOI: 10.1063/1.2382896  0.732
2006 Loparo JJ, Roberts ST, Tokmakoff A. Multidimensional infrared spectroscopy of water. I. Vibrational dynamics in two-dimensional IR line shapes. The Journal of Chemical Physics. 125: 194521. PMID 17129137 DOI: 10.1063/1.2382895  0.764
2006 Roberts ST, Loparo JJ, Tokmakoff A. Characterization of spectral diffusion from two-dimensional line shapes. The Journal of Chemical Physics. 125: 084502. PMID 16965024 DOI: 10.1063/1.2232271  0.714
2005 Eaves JD, Loparo JJ, Fecko CJ, Roberts ST, Tokmakoff A, Geissler PL. Hydrogen bonds in liquid water are broken only fleetingly. Proceedings of the National Academy of Sciences of the United States of America. 102: 13019-22. PMID 16135564 DOI: 10.1073/Pnas.0505125102  0.774
2005 Fecko CJ, Loparo JJ, Roberts ST, Tokmakoff A. Local hydrogen bonding dynamics and collective reorganization in water: ultrafast infrared spectroscopy of HOD/D(2)O. The Journal of Chemical Physics. 122: 54506. PMID 15740338 DOI: 10.1063/1.1839179  0.803
2004 Loparo JJ, Fecko CJ, Eaves JD, Roberts ST, Tokmakoff A. Reorientational and configurational fluctuations in water observed on molecular length scales Physical Review B - Condensed Matter and Materials Physics. 70: 1-4. DOI: 10.1103/Physrevb.70.180201  0.742
2004 Fecko CJ, Loparo JJ, Tokmakoff A. Generation of 45 femtosecond pulses at 3 μm with a KNbO3 optical parametric amplifier Optics Communications. 241: 521-528. DOI: 10.1016/J.Optcom.2004.07.038  0.728
2004 Fecko CJ, Eaves JD, Loparo JJ, Roberts ST, Tokmakoff A, Geissler PL. Dynamics of hydrogen bonds in water: Vibrational echoes and two-dimensional infrared spectroscopy Springer Series in Chemical Physics. 79: 535-538. DOI: 10.1007/3-540-27213-5_163  0.782
2004 Loparo JJ, Fecko CJ, Eaves JD, Roberts ST, Tokmakoff A. A unified analysis of ultrafast vibrational and orientational dynamics of HOD in D2O Springer Series in Chemical Physics. 79: 410-412. DOI: 10.1007/3-540-27213-5_126  0.766
2003 Fecko CJ, Eaves JD, Loparo JJ, Tokmakoff A, Geissler PL. Ultrafast hydrogen-bond dynamics in the infrared spectroscopy of water. Science (New York, N.Y.). 301: 1698-702. PMID 14500975 DOI: 10.1126/Science.1087251  0.797
2003 Loparo JJ, Cheatum CM, Ondrias MR, Simpson MC. Transient Raman observations of heme vibrational dynamics in five-coordinate iron porphyrins Chemical Physics. 286: 353-374. DOI: 10.1016/S0301-0104(02)00924-2  0.645
Show low-probability matches.