{"id":253,"date":"2024-10-22T01:00:18","date_gmt":"2024-10-22T05:00:18","guid":{"rendered":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/?page_id=253"},"modified":"2025-05-01T17:37:46","modified_gmt":"2025-05-01T21:37:46","slug":"publications","status":"publish","type":"page","link":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"253\" class=\"elementor elementor-253\">\n\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-82d7894 elementor-section-stretched elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"82d7894\" data-element_type=\"section\" data-e-type=\"section\" data-settings=\"{&quot;stretch_section&quot;:&quot;section-stretched&quot;,&quot;background_background&quot;:&quot;classic&quot;}\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-59ceb7c\" data-id=\"59ceb7c\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-76e5724 elementor-widget elementor-widget-heading\" data-id=\"76e5724\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h1 class=\"elementor-heading-title elementor-size-default\">Publications<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-3aea180 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"3aea180\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-07e7c9f\" data-id=\"07e7c9f\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-36b7cac elementor-widget elementor-widget-text-editor\" data-id=\"36b7cac\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h2>2025<\/h2>\n<hr>\n<p><b>Wenxuan Xu, Jin Qian, Dylan Collette, David Dunlap, Laura Finzi<\/b><br>\u201cInsights on the effect of macromolecular crowding on transcription and its regulation\u201d, Quarterly Reviews in Biophysics Discovery, 2025.<b>&nbsp;<a href=\"https:\/\/www.cambridge.org\/core\/journals\/qrb-discovery\/article\/insights-on-the-effect-of-macromolecular-crowding-on-transcription-and-its-regulation\/D85BC15B861145A99699D97388A2E34F\" target=\"_blank\" style=\"font-size: 1rem\">https:\/\/doi.org\/10.1017\/qrd.2025.8<\/a><\/b><\/p>\n<h2>2024<\/h2>\n<hr>\n<p><b>Jin Qian, Bing Wang, Irina Artsimovitch, David Dunlap, Laura Finzi<br><\/b>\u201cForce and the \u03b1-C-terminal domains bias RNA polymerase recycling\u201d,&nbsp;<em>Nature Comm<\/em>.<br><a style=\"font-size: 1rem\" href=\"https:\/\/www.nature.com\/articles\/s41467-024-51603-3\" target=\"_blank\" rel=\"noopener\"><b>https:\/\/www.nature.com\/articles\/s41467-024-51603-3.<\/b><\/a><\/p>\n<p><b>Jin Qian, Allison Cartee, Wenxuan Xu, Yan Yan, Bing Wang, Irina Artsimovitch, David Dunlap, Laura Finzi<\/b><br>\u201cReciprocating RNA Polymerase batters through roadblocks\u201d ,<em>Nature Comm<\/em>.,<br><a href=\"https:\/\/www.nature.com\/articles\/s41467-024-47531-x\" target=\"_blank\" rel=\"noopener\"><b>DOI:10.1038\/s41467-024-47531-x<\/b><\/a><strong>.<\/strong><\/p>\n<h2><span style=\"color: var(--ast-global-color-2);font-style: inherit;background-color: var(--ast-global-color-5)\">2023&nbsp;<\/span><\/h2>\n<hr>\n<p><b>Jin Qian, Dylan Collette, Irina Artsimovitch, David Dunlap, Laura Finzi<\/b><br>\u201cDetecting DNA Loops Using Tethered Particle Motion.\u201dIn: Heller, I., Dulin, D., Peterman, E.J. (eds) Single Molecule Analysis. Methods in Molecular Biology, vol 2694. Humana, New York, NY.<br><b><a href=\"https:\/\/doi.org\/10.1007\/978-1-0716-3377-9_21\" target=\"_blank\" rel=\"noopener\">DOI:10.1007\/978-1-0716-3377-9_21.<\/a><\/b><\/p>\n<p><b>Dylan Collette, David Dunlap and Laura Finzi<\/b><br>\u201cMacromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo\u201d, International Journal of Molecular Sciences, Review, in Special Issue \u201cRecent Advances in Genome Maintenance Studies.\u201d 2023, Volume 24, Issue 24, 17502. <b><a href=\"https:\/\/doi.org\/10.3390\/ijms242417502\" target=\"_blank\" rel=\"noopener\">DOI:10.3390\/ijms242417502 <\/a><\/b><\/p>\n<h2>2022<\/h2>\n<hr>\n<p><b> J. Qian, D. Dunlap, &amp; L. Finzi<\/b><br>&#8220;Thermodynamic Model of Bacterial Transcription&#8221; Phys. Rev. E, 2022.<br><b><a href=\"https:\/\/doi.org\/10.1103\/PhysRevE.106.044406\" target=\"_blank\" rel=\"noopener\">DOI:10.1103\/PhysRevE.106.044406<\/a><\/b><\/p>\n<p><b> W. Xu, Y. Yan, I.Artsimovitch, D. Dunlap, &amp; L. Finzi<\/b><br>&#8220;Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops&#8221;, Nucleic Acids Research, 2022.<br><b><a href=\"https:\/\/doi.org\/10.1093\/nar\/gkac093\" target=\"_blank\" rel=\"noopener\">DOI: 10.1063\/10.0006622<\/a><\/b><\/p>\n<p><b> Y. Lu, G. Borjas, C. Hendrickson, Z.V\u00f6r\u00f6, D. Dunlap, K. Shearwin &amp; L. Finzi<\/b><br>&#8220;RNA polymerase efficiently transcribes through DNA-scaffolded, cooperative bacteriophage repressor complexes&#8221;, FEBS Letters, 2022.<br><b><a href=\"https:\/\/doi.org\/10.1002\/1873-3468.14447\" target=\"_blank\" rel=\"noopener\">DOI: 10.1002\/1873-3468.14447 <\/a><\/b><\/p>\n<h2>2021<\/h2>\n<hr>\n<p><b> J. Qian, W. Xu, D. Dunlap, &amp; L. Finzi<\/b><br>&#8220;Single-molecule insights into torsion and roadblocks in bacterial transcript elongation&#8221;, Transcription, 2021.<br><b><a href=\"https:\/\/doi.org\/10.1080\/21541264.2021.1997315\" target=\"_blank\" rel=\"noopener\">DOI: 10.1080\/21541264.2021.1997315 <\/a><\/b><\/p>\n<p><b> A. Zhang, Y .Yan, F .Leng, D. Dunlap, &amp; L. Finzi<\/b><br>&#8220;Ionic strength modulates HU protein-induced DNA supercoiling&#8221;, Posted on BioRxiv, 2021.<br><b><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.10.14.464438v1\" target=\"_blank\" rel=\"noopener\">&nbsp;DOI: 10.1101\/2021.10.14.464438 <\/a><\/b><\/p>\n<p><b> Y. Yan, W. Xu, S. Kumar, A. Zhang, F. Leng, D. Dunlap, &amp; L. Finzi<\/b><br>&#8220;Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time&#8221;, Nucleic Acids Research, 2021.<b><a href=\"https:\/\/doi.org\/10.1093\/nar\/gkab946\" target=\"_blank\" rel=\"noopener\">DOI: 10.1093\/nar\/gkab946 <\/a><\/b><\/p>\n<p><b> J. Piccolo, J.M. Harper, D. McCalla, W. Xu, S. Miller, J. Doan, D.T. Kovari, D. Dunlap, &amp; L. Finzi<\/b><br>&#8220;Force spectroscopy with electromagnetic tweezers&#8221;, Journal of Applied Physics, 2021.<b><a href=\"https:\/\/aip.scitation.org\/doi\/full\/10.1063\/5.0060276\" target=\"_blank\" rel=\"noopener\">DOI: 10.1063\/5.0060276 <\/a><\/b><\/p>\n<p><b> W.Xu, D. Dunlap, &amp; L. Finzi<\/b><br>&#8220;Energetics of twisted DNA topologies&#8221;, Biophysical Journal, 2021.&nbsp;<b><a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2021.05.002\" target=\"_blank\" rel=\"noopener\">DOI: 10.1016\/j.bpj.2021.05.002 <\/a><\/b><\/p>\n<p><b> W.Xu, D. Dunlap, &amp; L. Finzi<\/b><br>&#8220;Tethered Particle Microscopy&#8221;, Encyclopedia of Biophysics, 2021.&nbsp;<b><a href=\"https:\/\/doi.org\/10.1007\/978-3-642-35943-9_489-1\" target=\"_blank\" rel=\"noopener\">DOI: 10.1007\/978-3-642-35943-9_489-1 <\/a><\/b><\/p>\n<p><b> D. Salerno, F. Mantegazza, V. Cassina, M. Cristofalo, Q. Shao, L. Finzi, &amp; D. Dunlap<\/b><br>&#8220;Nanomechanics of negatively supercoiled diamino purine-substituted DNA&#8221;, Nucleic Acids Research, 2021.<br><b><a href=\"https:\/\/doi.org\/10.1093\/nar\/gkab982\" target=\"_blank\" rel=\"noopener\">DOI: 10.1093\/nar\/gkab982 <\/a><\/b><\/p>\n<p><b> J. Qian, D. Dunlap, &amp; L. Finzi<\/b><br>&#8220;Basic mechanisms and kinetics of pause-interspersed transcript elongation&#8221;, Nucleic Acids Research, 2021.<br><b><a href=\"https:\/\/doi.org\/10.1093\/nar\/gkaa1182\" target=\"_blank\" rel=\"noopener\">DOI: 10.1093\/nar\/gkaa1182 <\/a><\/b><\/p>\n<h2><span style=\"font-weight: normal\">2019<\/span><b>&nbsp;<\/b><\/h2>\n<hr>\n<p><b> DT Kovari, D. Dunlap, ER Weeks, &amp; L. Finzi<\/b><br>&#8220;Model-free 3D localization with precision estimates for brightfield imaged particles&#8221;, Optics Express,<b><a href=\"https:\/\/doi.org\/10.1364\/OE.27.029875\" target=\"_blank\" rel=\"noopener\">Optics Express: Vol. 27, Issue 21, pp. 29875-29895 (2019) <\/a><\/b><\/p>\n<p><b> Cristofalo, M., Kovari, D., Corti, R., Salerno, D., Cassina, V., Dunlap, D., &amp; Mantegazza, F. <\/b><br>&#8220;Nanomechanics of diamino purine-substituted DNA&#8221;, Biophysical journal, 2019.<b><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0006349519300633\" target=\"_blank\" rel=\"noopener\">DOI: 10.1016\/j.bpj.2019.01.027 <\/a><\/b><\/p>\n<h2><b>2018&nbsp;<\/b><\/h2>\n<hr>\n<p><b> S. Sarkar, S. Goyal, N. Gao, J. Mack, B. Thompson, D. Dunlap, K. Chattopadhyay, L. Finzi <\/b><br>&#8220;Specifically bound Lambda repressor dimers promote adjacent non-specific binding&#8221;, PLOS One, 2018.<b><a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0194930\" target=\"_blank\" rel=\"noopener\">PLoS ONE 13(4): e0194930 <\/a><\/b><\/p>\n<p><b> Y. Yan, Y. Ding, F. Leng, D. Dunlap, L. Finzi<\/b><br>&#8220;Protein-mediated loops in supercoiled DNA create large topological domains&#8221;, Nucleic Acids Research, 2018.<br><b><a href=\"https:\/\/academic.oup.com\/nar\/advance-article\/doi\/10.1093\/nar\/gky153\/4925756\" target=\"_blank\" rel=\"noopener\">DOI: 10.1093\/nar\/gky153 <\/a><\/b><\/p>\n<p><b> Y. Yan, F. Leng, L. Finzi, D. Dunlap<\/b><br>&#8220;Protein-mediated looping of DNA under tension requires supercoiling&#8221;, Nucleic Acids Research, 2018.&nbsp;<b><a href=\"https:\/\/academic.oup.com\/nar\/advance-article\/doi\/10.1093\/nar\/gky021\/4818921\" target=\"_blank\" rel=\"noopener\">DOI:10.1093\/nar\/gky021 <\/a><\/b><\/p>\n<p><b> D.T. Kovari, Y. Yan, L. Finzi, D. Dunlap<\/b><br>&#8220;Tethered Particle Motion: An Easy Technique for Probing DNA Topology and Interactions with Transcription Factors&#8221; in &#8220;Methods in Molecular biology: Single-Molecule Analysis: Methods and Protocols&#8221;, ed. E.J.G. Peterman, series editor John Walker, vol 1665, Humana Press, New York, NY, p317-340 (2018).&nbsp;<b><a href=\"https:\/\/link.springer.com\/protocol\/10.1007\/978-1-4939-7271-5_17\" target=\"_blank\" rel=\"noopener\">DOI: 10.1007\/978-1-4939-7271-5_17<\/a><\/b><\/p>\n<h2>2017<\/h2>\n<hr>\n<p><b>Z. V\u00f6r\u00f6s, Y. Yan, D. Kovari, L. Finzi, D. Dunlap<\/b><br>&#8220;Proteins mediating DNA loops effectively block transcription&#8221;, Protein Science, 2017.&nbsp;<b><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/pro.3156\/full\" target=\"_blank\" rel=\"noopener\">DOI: 10.1002\/pro.3156<\/a><\/b><\/p>\n<p><b>Suleyman Ucuncuoglu, David A. Schneider, Eric Weeks, David Dunlap, Laura Finzi<\/b> &#8220;Multiplexed, Tethered Particle Microscopy for Studies of DNA-Enzyme Dynamics&#8221;, Methods in Enzymology, vol. &#8220;Single-molecule Enzymology&#8221;<br><b>h<a style=\"font-size: 1rem\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0076687916302555?via%3Dihub\" target=\"_blank\" rel=\"noopener\">ttps:doi\/.org\/10.1016\/bs.mie.2016.08.008<\/a><\/b><\/p>\n<h2><b>2016<\/b><\/h2>\n<hr>\n<p><b>S. Ucuncuoglu, K. L. Engel, P. K. Purohit, D. D. Dunlap, D. A. Schneider, L. Finzi<\/b><br>&#8220;Direct characterization of transcription elongation by RNA polymerase I&#8221; Plos One, 2016.<br><b><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/27455049\" target=\"_blank\" rel=\"noopener\">DOI:10.1371\/journal.pone.0159527. eCollection 2016<\/a><\/b><\/p>\n<p><b>Laura Finzi and Wilma K. Olson<\/b><br>&#8220;The emerging role of DNA supercoiling as a dynamic player in genomic structure and function&#8221; Biophysics Reviews, 2016. <b><a href=\"https:\/\/link.springer.com\/article\/10.1007\/s12551-016-0214-x\" target=\"_blank\" rel=\"noopener\">DOI:10.1007\/s12551-016-0214-x<\/a><\/b><\/p>\n<p><b>Laura Finzi and David D. Dunlap<\/b><br>&#8220;supercoiling biases the formation of loops involved in gene regulation&#8221; Biophysics Reviews, 2016.<br><b><a href=\"https:\/\/link.springer.com\/article\/10.1007\/s12551-016-0211-0\" target=\"_blank\" rel=\"noopener\">DOI:10.1007\/s12551-016-0211-0<\/a><\/b><\/p>\n<p><b>Suleyman Ucuncuoglu, David A. Schneider, Eric Weeks, David Dunlap, and Laura Finzi<\/b><br>&#8220;Multiplexed, tethered particle microscopy for studies of DNA-enzyme dynamics&#8221; Methods in Enzymology, 2016. <b><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0076687916302555\" target=\"_blank\" rel=\"noopener\">DOI:10.1016\/bs.mie.2016.08.008<\/a><\/b><\/p>\n<h2>2015<\/h2>\n<hr>\n<p><b>M.Fernandez, Q. Shao, C.Fountain, L. Finzi, and D. Dunlap<\/b><br>&#8220;E. coli gyrase fails to negatively supercoil diaminopurine-substituted DNA&#8221; Journal of Molecular Biology, 2015. <b><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0022283615002478\" target=\"_blank\" rel=\"noopener\">DOI:10.1016\/j.jmb.2015.04.006<\/a><\/b><\/p>\n<h2>2014<\/h2>\n<hr>\n<p><b>Y.Ding, C. Manzo, G.Flucrand, F.leng, D. Dunlap, and L. Finzi<\/b><br>&#8220;DNA supercoiling: A regulatory signal for the Lambda repressor&#8221; PNAS, 2014.&nbsp;<b><a href=\"https:\/\/www.pnas.org\/content\/early\/2014\/10\/15\/1320644111\" target=\"_blank\" rel=\"noopener\">DOI: 10.1073\/pnas.1320644111<\/a><\/b><\/p>\n<p><b>D.Priest, S.Kumar, Y.Yan, D.Dunlap, I.Dodd, K.Shearwin<\/b><br>&#8220;Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E.coli cells&#8221; PNAS, 2014.<br><b><a href=\"https:\/\/www.pnas.org\/content\/early\/2014\/10\/02\/1410764111.abstract\" target=\"_blank\" rel=\"noopener\">DOI: 10.1073\/pnas.1410764111<\/a><\/b><\/p>\n<p><b>S.Kumar, C. Manzo, C.Zurla, S.Ucuncuoglu, L. Finzi, and D. Dunlap<\/b><br>&#8220;Enhanced tethered-particle motion analysis reveals viscous effects&#8221; Biophys J, 2014.&nbsp;<b><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24461015\" target=\"_blank\" rel=\"noopener\">DOI: 10.1016\/j.bpj.2013.11.4501<\/a><\/b><\/p>\n<h2>2013<\/h2>\n<hr>\n<p><b>M.A. Mendes, R.F. Guerra, M.C. Berns, C. Manzo, S. Masiero, L. Finzi, M. M. Kater, and L. Colombo<\/b><br>&#8220;MADS Domain Transcription Factors Mediate Short-Range DNA Looping That Is Essential for Target Gene Expression in Arabidopsis&#8221; The Plant Cell, 2013.&nbsp;<b><a href=\"https:\/\/db.cngb.org\/search\/literature\/23847151\/?u_if=YzdmNTVkNmE4MTA3Njg4MDQyNDBkZjZhOGFmNTdlNzd8Y25nYnwoQmVybnMgTUMpW0F1dGhvcl0%3D&amp;pos=2\">DOI:10.1105\/tpc.112.108688<\/a><\/b><\/p>\n<p><b>N. Gao, K.E. Shearwin, J. Mack, L. Finzi, and D. Dunlap<\/b><br>&#8220;Purification of Bacteriophage Lambda Repressor&#8221; Protein Expression and Purification, 2013.&nbsp;<b><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1046592813001198\" target=\"_blank\" rel=\"noopener\">DOI:10.1016\/j.pep.2013.06.013<\/a><\/b><\/p>\n<p><b>H. Wang, I.B. Dodd, D.D. Dunlap, K.E. Shearwin, and L. Finzi<\/b><br>&#8220;Single-molecule analysis of DNA wrapping and looping by a circular 14mer wheel of the bacteriophage 186 CI repressor&#8221; NAR, 2013.&nbsp;<b><a href=\"https:\/\/nar.oxfordjournals.org\/content\/early\/2013\/04\/24\/nar.gkt298.abstract\" target=\"_blank\" rel=\"noopener\">DOI: 10.1093\/nar\/gkt298.<\/a><\/b><\/p>\n<p><b>L. Finzi and D. Dunlap<\/b><br>&#8220;Tethered particle Microscopy (TPM)&#8221; in &#8220;Encyclopedia of Biophysics&#8221;, Springer (Berlin Heidelberg), 2579-2582 (2013).&nbsp;<b><a href=\"https:\/\/link.springer.com\/referenceworkentry\/10.1007\/978-3-642-16712-6_489\">Tethered particle Microscopy (TPM)<\/a><\/b><\/p>\n<h2>2012<\/h2>\n<hr>\n<p><b>C. Manzo, C. Zurla, D. Dunlap, and L. Finzi<\/b><br>&#8220;The effect of non-specific binding of lambda repressor on DNA looping dynamics&#8221; Biophys. J.,103(8),1753,2012.<br><b><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0006349512010181\" target=\"_blank\" rel=\"noopener\">DOI: 10.1016\/j.bpj.2012.09.006.<\/a><\/b><\/p>\n<p><b>S. Goyal, C. Foutain, D. Dunlap, F. Family, and L. Finzi<\/b><br>&#8220;Stretching DNA to quantify nonspecific protein binding&#8221; Phys. Rev. E, 2012.&nbsp;<b><a href=\"https:\/\/pre.aps.org\/abstract\/PRE\/v86\/i1\/e011905\" target=\"_blank\" rel=\"noopener\">DOI: 10.1103\/PhysRevE.86.011905.<\/a><\/b><\/p>\n<p><b>Q. Shao, S. Goyal, L. Finzi, and D. Dunlap<\/b><br>&#8220;Physiological Levels of Salt and Polyamines Favor Writhe and Limit Twist in DNA&#8221; Macromolecules, 2012.&nbsp;<b><a href=\"https:\/\/pubs.acs.org\/doi\/full\/10.1021\/ma300211t\" target=\"_blank\" rel=\"noopener\">DOI: 10.1021\/ma300211t.<\/a><\/b><\/p>\n<h2>2011<\/h2>\n<hr>\n<p><b>D. Lewis, P. Le, C. Zurla, L. Finzi, and S. Adhya<\/b><br>&#8220;Multilevel autoregulation of lambda repressor protein CI by DNA looping in vitro&#8221; PNAS, 2011.&nbsp;<b><a href=\"https:\/\/www.pnas.org\/content\/early\/2011\/08\/18\/1111221108\/\" target=\"_blank\" rel=\"noopener\">DOI: 10.1073\/pnas.1111221108<\/a><\/b><\/p>\n<p><b>D. Dunlap, C. Zurla, C. Manzo and L. Finzi<\/b><br>&#8220;Probing DNA Topology Using Tethered Particle Motion&#8221; in &#8220;Methods in Molecular Biology: Single-Molecule Analysis: Methods and Protocols&#8221; eds. E.J.G. Peterman and G Wuite, series editor John Walker, Springer vol. 783, pp. 295-313, 2011.<br><b><a href=\"https:\/\/www.springerprotocols.com\/Abstract\/doi\/10.1007\/978-1-61779-282-3_16\" target=\"_blank\" rel=\"noopener\">DOI 10.1007\/978-1-61779-282-3_16<\/a><\/b><\/p>\n<h2>2010<\/h2>\n<hr>\n<p><b>L. Finzi, C. Manzo, C. Zurla, H. Wang, D. Lewis, S. Adhya and D. Dunlap<\/b><br>&#8220;DNA Looping in Prophage Lambda: New Insight from Single-Molecule Microscopy&#8221; in &#8220;Biophysics of DNA-protein interactions: From single molecules to biological systems&#8221;Eds. M. Williams and L. J Maher, Springer pp. 193-212, 2010.<br><b><a href=\"https:\/\/www.springerlink.com\/content\/l214131480472806\/\" target=\"_blank\" rel=\"noopener\">DOI 10.1007\/978-0-387-92808-1<\/a><\/b><\/p>\n<p><b>Paul Liebesny, Sachin Goyal, David Dunlap, Fereydoon Family and Laura Finzi<\/b><br>&#8220;Determination of the Number of Protein Bound non-specifically to DNA, Journal of Physics: Condensed Matter,<b><a href=\"https:\/\/iopscience.iop.org\/0953-8984\/22\/41\/414104\" target=\"_blank\" rel=\"noopener\"><br>DOI:10.1088\/0953-8984\/22\/41\/414104&nbsp;<\/a><\/b><\/p>\n<p><b>L. Finzi and D. Dunlap<\/b><br>&#8220;Single-molecule approaches to structure, kinetics and thermodynamics of transcriptional regulatory nucleoprotein complexes, minireview, Journal of Biological Chemistry.&nbsp;<b><a href=\"https:\/\/www.jbc.org\/content\/285\/25\/18973.full.pdf+html\" target=\"_blank\" rel=\"noopener\">DOI:10.1074\/jbc.R109.062612&nbsp;<\/a><\/b><\/p>\n<p><b>C. Manzo and L. Finzi<\/b><br>&#8220;Quantitative analysis of DNA looping kinetics from tethered particle motion experiments&#8221;<b><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0076687910750096?via%3Dihub\">Methods in Enzymology, Ed. Nils G. Walter, 2010<\/a><\/b><\/p>\n<p><b>D. E. A. Lewis, S. J. Lee, S. Semsey, K. Virnik, L. Finzi and S. Adhya <\/b><br>&#8220;Role of HU in the regulation of gal promoters&#8221; in &#8221; Bacterial Chromatin&#8221; Eds: C. Dorman and R. T. Dame, Springer, 2010.<b><a href=\"https:\/\/www.springerlink.com\/content\/vj4132u645p78423\/\" target=\"_blank\" rel=\"noopener\"><br>DOI: 10.1007\/978-90-481-3473-1_17<\/a><\/b><\/p>\n<h2>2009<\/h2>\n<hr>\n<p><b>H. Wang, L. Finzi, D. E. A. Lewis, D. D. Dunlap<\/b><br>&#8220;AFM Studies of Lambda Repressor Oligomers Securing DNA Loops&#8221; <b><a href=\"https:\/\/www.ingentaconnect.com\/content\/ben\/cpb\/2009\/00000010\/00000005\/art00005\" target=\"_blank\" rel=\"noopener\">Current Pharmaceutical Biotechnology, 10, 494-501 (2009)<\/a><\/b><\/p>\n<p><b>C. Zurla, C. Manzo, D. D. Dunlap, D. E. A. Lewis, S. Adhya, L. Finzi<\/b><br>&#8220;Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor. <em>Nucleic Acids Research&#8221;<\/em>.<br><b><a href=\"https:\/\/nar.oxfordjournals.org\/cgi\/content\/abstract\/37\/9\/2789\" target=\"_blank\" rel=\"noopener\">&nbsp;DOI:10.1093\/nar\/gkp134 (2009)<\/a><\/b><\/p>\n<p><b>L. Finzi<br><\/b><span style=\"font-style: inherit;background-color: var(--ast-global-color-5)\"><span style=\"font-weight: inherit\">Benham, C. J., Harvey, S., Olson, W. K., Sumners, D. L., &amp; Swigon, D. (2011).&#8221; Perspectives on DNA looping. In C. J. Benham, S. Harvey, W. K. Olson, D. L. Sumners, &amp; D. Swigon (Eds.), Mathematics of DNA structure, function, and interactions. Springer Science+Business Media, LLC&#8221;.<\/span><br><\/span><b style=\"font-style: inherit;background-color: var(--ast-global-color-5)\"><a href=\"https:\/\/www.springer.com\/mathematics\/mathematical+biology\/book\/978-1-4419-0669-4\" target=\"_blank\" rel=\"noopener\">DOI 10.1007\/978-1-4419-0670-0<\/a><\/b><\/p>\n<h2>2008<\/h2>\n<hr>\n<p><b>G. Lia, M. Indrieri, T. Owen-Hughes, L. Finzi, A. Podesta&#8217;, P. Milani, D.Dunlap<\/b><br>&#8220;ATP-dependent looping of DNA by ISWI&#8221;, Special issue:&#8221; From single molecules and single cells to tissue imaging&#8221;&nbsp;<b><a href=\"https:\/\/www3.interscience.wiley.com\/journal\/121369881\/abstract?CRETRY=1&amp;SRETRY=0\" target=\"_blank\" rel=\"noopener\">Journal of Biophotonics 4,280-286 (2008)<\/a><\/b><\/p>\n<p><b>G. Lia, S. Semsey, D. e. lewis, S. Adhya, D. Besinmon, D. Dunlap, L. Finzi<\/b><br>&#8220;The Antiparallel loops in Gal DNA&#8221;&nbsp;<em>Nucleic Acids Research<\/em>, 36, 4204\u20134210.&nbsp;<a href=\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC2475638\/\" target=\"_blank\" rel=\"noopener\"><b>https:\/\/doi.org\/10.1093\/nar\/gkn361<\/b><\/a><b><\/b><\/p>\n<h2>2007<\/h2>\n<hr>\n<p><b>C. Zurla, G. Bertoni, F. Valle, G. Dietler, L. Finzi, D. Dunlap<\/b><br>&#8220;Architectural role of IHF in the regulation of transcription at the single molecule level&#8221;&nbsp;<b><a href=\"https:\/\/www.sciencedirect.com\/science?_ob=ArticleURL&amp;_udi=B6TFB-4NMSRY4-1&amp;_user=655046&amp;_coverDate=07%2F31%2F2007&amp;_rdoc=17&amp;_fmt=high&amp;_orig=browse&amp;_origin=browse&amp;_zone=rslt_list_item&amp;_srch=doc-info(%23toc%235222%232007%23998719997%23659678%23FLA%23display%23Volume)&amp;_cdi=5222&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_ct=18&amp;_acct=C000034138&amp;_version=1&amp;_urlVersion=0&amp;_userid=655046&amp;md5=d6c80c2d86ec6dcb7194738e2ee5b0f6&amp;searchtype=a\" target=\"_blank\" rel=\"noopener\">Biophysical Chemistry 128, 245 &#8211; 252 (2007)<\/a><\/b><\/p>\n<p><b>F. Guerra, L. Imperadori, D. Dunlap, R. Mantovani, L. Finzi<\/b><br>&#8220;DNA Compaction by the nuclear factor-Y&#8221;&nbsp;<b><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0006349507712699\">Biophy. J., 93(1):176-182 (2007)<\/a><\/b><\/p>\n<p><b>J. F. Beausang, C. Zurla, C. Manzo, D. Dunlap, L. Finzi, and P. Nelson <\/b><br>&#8220;DNA Looping Kinetics Analyzed Using Diffusive Hidden Markov Model&#8221;&nbsp;<b><a href=\"https:\/\/www.sciencedirect.com\/science?_ob=ArticleURL&amp;_udi=B94RW-4V9YVV0-2&amp;_user=655046&amp;_coverDate=04%2F15%2F2007&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_searchStrId=1503431197&amp;_rerunOrigin=scholar.google&amp;_acct=C000034138&amp;_version=1&amp;_urlVersion=0&amp;_userid=655046&amp;md5=f0406447279b52ab5da4eaca955a47e5&amp;searchtype=a\" target=\"_blank\" rel=\"noopener\">Biophys. J. &#8211; 92:L64-L66 (2007)<\/a><\/b><\/p>\n<h2>2006<\/h2>\n<hr>\n<p><b>J. F. Beausang, C. Zurla, L. Sullivan, L. Finzi, P. C. Nelson<\/b><br>&#8220;Elementary simulation of tethered Brownian motion&#8221;&nbsp;<b><a href=\"https:\/\/arxiv.org\/abs\/q-bio\/0610007\" target=\"_blank\" rel=\"noopener\">AJP q-bio.BM\/0610007<\/a><\/b><\/p>\n<p><b>P. Nelson, C. Zurla, D. Brogioli, J. F. Beausang, L. Finzi, and D. Dunlap<\/b><br>&#8220;Tethered Particle Motion as a Diagnostic of DNA Tether Length&#8221;&nbsp;<b><a href=\"https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/jp0630673\" target=\"_blank\" rel=\"noopener\">The Journal of Physical Chemistry B, 110 (34): 17260-17267 (2006)<\/a><\/b><\/p>\n<p><b>C. Zurla, A Franzini, G. Galli, D.D. Dunlap, D.E.A. Lewis, S. Adhya and L. Finzi<\/b><br>&#8220;Novel tethered particle motion analysis of CI protein-mediated DNA looping in the regulation of bacteriophage lambda&#8221;<br><b><a href=\"https:\/\/iopscience.iop.org\/0953-8984\/18\/14\/S07\" target=\"_blank\" rel=\"noopener\">Journal of Physics:Condensed Matter, 18, S225-S234 (2006)<\/a><\/b><\/p>\n<h2>2005<\/h2>\n<hr>\n<p><b>A. Podesta M. Indrieri, D. Brogioli, J. S. Manning, P. Milani, R. Guerra, L. Finzi, D. Dunlap<\/b><br>&#8220;Positively charged surfaces increase the flexibility of DNA&#8221;&nbsp;<b><a href=\"https:\/\/www.sciencedirect.com\/science?_ob=ArticleURL&amp;_udi=B94RW-4TT2KGX-19&amp;_user=655046&amp;_coverDate=10%2F31%2F2005&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_searchStrId=1389189709&amp;_rerunOrigin=scholar.google&amp;_acct=C000034138&amp;_version=1&amp;_urlVersion=0&amp;_userid=655046&amp;md5=cc088e3fecec2fe99626d1f0bdd0841d\" target=\"_blank\" rel=\"noopener\">Biophys J., 89:2558-2563 (2005)<\/a><\/b><\/p>\n<p><b>E. Consoli, R. Croce, D. Brogioli, D. Dunlap and L. Finzi<\/b><br>&#8220;Diffusion of phosphorylated and non-phosphorylated Light Harvesting Complex II in the thylakoid membranes&#8221;<br><b><a href=\"https:\/\/www.nature.com\/embor\/journal\/v6\/n8\/abs\/7400464.html\" target=\"_blank\" rel=\"noopener\">EMBO reports, 6(8):782-6 (2005)<\/a><\/b><\/p>\n<p><b>G. Garab, P. Galaida, I. Pomozi, L. Finzi, T. Praznovszky, P. Ormos, H. Van Amerongen<\/b><br>&#8220;Alignment of biological microparticles by polarized laser beam&#8221;&nbsp;<b><a href=\"https:\/\/www.springerlink.com\/content\/x33423473l421nph\/\" target=\"_blank\" rel=\"noopener\">Eur. Biophys. J., 34(4):335-43 (2005)<\/a><\/b><\/p>\n<p><b>M. Kooiker, C. Airoldi, A. Losa, P.S. Manzotti, L. Finzi, M. M. Kater and L. Colombo<\/b><br>&#8220;Basic pentacysteine1 a GA-Binding Protein that Induces Conformational Changes in the Regulatory Region of the Homeotic Arabidopsis Gene SEEDSTICK&#8221; <b><a href=\"https:\/\/www.plantcell.org\/cgi\/content\/abstract\/17\/3\/722\" target=\"_blank\" rel=\"noopener\">The Plant Cell, 17:722-729 (2005)<\/a><\/b><\/p>\n<h2>2004<\/h2>\n<hr>\n<p><b>A. Podesta L. Imperadori, W. Colnaghi, L. Finzi, P. Milani and D. D. Dunlap<\/b><br>&#8220;Atomic Force Microscopy studies of DNA deposited on poly-L-ornithine coated mica&#8221;&nbsp;<b><a href=\"https:\/\/www3.interscience.wiley.com\/journal\/118757043\/abstract\" target=\"_blank\" rel=\"noopener\">Journal of Microscopy 215:236-240 (2004<\/a>)<\/b><\/p>\n<h2>2003<\/h2>\n<hr>\n<p><b>G. Lia, D. Bensimon, V. Croquette, J-F. Allemand, D. Dunlap, DAE. Lewis, S. Adhya, L. Finzi<\/b><br>&#8220;Supercoiling and denaturation in GalR\/HU-mediated DNA looping as seen by single-molecule microscopy&#8221;&nbsp;<b><a href=\"https:\/\/www.pnas.org\/content\/100\/20\/11373.abstract\" target=\"_blank\" rel=\"noopener\">PNAS, 100:11373-377 (2003)<\/a><\/b><\/p>\n<p><b>L. Finzi and D. Dunlap<\/b><br>&#8220;Single molecule studies of DNA architectural changes induced by regulatory proteins&#8221;. In S. Adhya &amp; S. Garges (Eds.), <em>Methods in Enzymology<\/em> (Vol. 370, pp. 369\u2013378). Elsevier.&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/14712660\/\" target=\"_blank\" rel=\"noopener\"><b>https:\/\/doi.org\/10.1016\/S0076-6879(03)70033-2<\/b><\/a><\/p>\n<h2>2002<\/h2>\n<hr>\n<p><b>M. Capitanio, G. Romano, R. Ballerini, D. Dunlap, L. Finzi, M. Giuntini and F.S. Pavone<\/b><br>&#8220;Calibration of an Optical Tweezer with DIC Signals&#8221;&nbsp;<b><a href=\"https:\/\/rsi.aip.org\/rsinak\/v73\/i4\/p1687_s1\" target=\"_blank\" rel=\"noopener\">Reviews of Scientific Instruments, 73:1687-1696 (2002)<\/a><\/b><\/p>\n<h2>2001<\/h2>\n<hr>\n<p><b>L. Finzi, P. Galajda, and G. Garab<\/b><br>&#8220;Labeling phosphorylated LHCII with microspheres for tracking studies and force measurements&#8221;&nbsp;<b><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1011134401002305\">J. Photochem. Photobiol B:Biology, 65:1-4 (2001)<\/a><\/b><\/p>\n<p><b>L. Sacconi, G. Romano, R. Ballerini, M. Capitanio, M. De Pas, D. Dunlap, M. Giuntini, L. Finzi and F.S. Pavone<\/b><br>&#8220;Finzi, L., &amp; Dunlap, D. (2001). A 3D micro-TOP magneto-optical trap for micro-objects manipulation. <em>Optics Letters<\/em>, 26, 1359\u20131361&#8243;&nbsp;<b><a target=\"_new\" rel=\"noopener\">h<\/a><a style=\"font-size: 1rem\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/18049608\/\" target=\"_blank\" rel=\"noopener\">ttps:\/\/doi.org\/10.1364\/OL.26.001359<\/a><\/b><\/p>\n<h2>1995<\/h2>\n<hr>\n<p><b>L. Finzi and J. Gelles<\/b><br>&#8220;<span style=\"background-color: var(--ast-global-color-5);font-size: 1rem;font-weight: inherit\">Measurement of Lac repressor-mediated loop formation and breakdown in single DNA molecules. <\/span><em style=\"background-color: var(--ast-global-color-5);font-size: 1rem;font-weight: inherit\">Science<\/em><span style=\"background-color: var(--ast-global-color-5);font-size: 1rem;font-weight: inherit\">, 267(5197), 378\u2013380.<\/span><span style=\"font-style: inherit;font-weight: inherit;background-color: var(--ast-global-color-5)\">&#8220;<br><\/span><a style=\"font-size: 1rem\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/7824935\/\" target=\"_blank\" rel=\"noopener\"><b>https:\/\/doi.org\/10.1126\/science.7809630<\/b><\/a><\/p>\n<h2>1992<\/h2>\n<hr>\n<p><b>S.B. Smith, L. Finzi and C. Bustamante<br><\/b>&#8220;Direct mechanical measurements of the elasticity of single DNA molecules using magnetic beads&#8221;. <em>Science<\/em>, 258(5085), 1122.<br><a style=\"font-size: 1rem\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/1439819\/\" target=\"_blank\" rel=\"noopener\"><b>https:\/\/doi.org\/10.1126\/science.1326609<\/b><\/a><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Publications 2025 Wenxuan Xu, Jin Qian, Dylan Collette, David Dunlap, Laura Finzi\u201cInsights on the effect of macromolecular crowding on transcription and its regulation\u201d, Quarterly Reviews in Biophysics Discovery, 2025.&nbsp;https:\/\/doi.org\/10.1017\/qrd.2025.8 2024 Jin Qian, Bing Wang, Irina Artsimovitch, David Dunlap, Laura Finzi\u201cForce and the \u03b1-C-terminal domains bias RNA polymerase recycling\u201d,&nbsp;Nature Comm.https:\/\/www.nature.com\/articles\/s41467-024-51603-3. Jin Qian, Allison Cartee, Wenxuan Xu, [&hellip;]<\/p>\n","protected":false},"author":4,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"site-sidebar-layout":"no-sidebar","site-content-layout":"page-builder","ast-site-content-layout":"full-width-container","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"disabled","ast-breadcrumbs-content":"","ast-featured-img":"disabled","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"default","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"set","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":""},"class_list":["post-253","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/pages\/253","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/comments?post=253"}],"version-history":[{"count":0,"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/pages\/253\/revisions"}],"wp:attachment":[{"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/media?parent=253"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}