{"id":247,"date":"2024-10-21T20:54:43","date_gmt":"2024-10-22T00:54:43","guid":{"rendered":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/?p=247"},"modified":"2026-02-10T16:24:58","modified_gmt":"2026-02-10T21:24:58","slug":"transcription-and-related-molecular-motors","status":"publish","type":"post","link":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/transcription-and-related-molecular-motors\/","title":{"rendered":"Transcription"},"content":{"rendered":"\t\t
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Living organisms thrive, grow and reproduce thanks to a well-regulated transcription program. We wish to understand the physical laws that underlie regulatory mechanisms. This is a multifaceted problem that involves understanding the mechanical properties of DNA in different environments and how such properties affect DNA interaction with proteins, including molecular motors that carry out, or affect, transcription. New techniques and methods of analysis need to be constantly developed to probe the complex interaction between template and machinery. The knowledge gathered can be harnessed to pave the way for new treatments of diseases and new medical technology.<\/p>

In this context, we are investigating how a transcribing RNA polymerase is affected by proteins bound on the template DNA, protein-induced DNA topology, supercoiling, tension, crowding and condensates.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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Relevant Publications<\/h2>
Authors<\/strong><\/td>Title<\/strong><\/td>Journal<\/strong><\/td>Volume<\/strong><\/td>Pages<\/strong><\/td>Year<\/strong><\/td><\/tr>
Jin Qian, Bing Wang, Irina Artsimovitch, David Dunlap, Laura Finzi<\/td>“Force and the \u03b1-C-terminal domains bias RNA polymerase recycling”<\/td>Nature Communications<\/td>\u00a0_<\/td>_<\/td>2024<\/td><\/tr>
Jin Qian, Allison Cartee, Wenxuan Xu, Yan Yan, Bing Wang, Irina Artsimovitch, David Dunlap, Laura Finzi<\/td>“Reciprocating RNA Polymerase batters through roadblocks”<\/td>Nature Communications<\/td>\u00a0_<\/td>_<\/td>2024<\/td><\/tr>
Jin Qian, David Dunlap, Laura Finzi<\/td>\u201cA Thermodynamic Model of Bacterial Transcription\u201d<\/td>Physical Review E<\/td>\u00a0_<\/td>\u00a0_<\/td>2022<\/td><\/tr>

Wenxuan Xu, Yan Yan, Irina Artsimovich, David Dunlap, Laura Finzi<\/p><\/td>

\u201cPositive supercoiling favors transcription elongation through lac repressor-mediated DNA loops\u201d<\/td>Nucleic Acids Research<\/i><\/td>\u00a0_<\/td>\u00a0_<\/td>2022<\/td><\/tr>

Yue Lu, Gustavo Borjas, Cristine Hendrickson, Zsuzsanna V\u00f6r\u00f6s, David Dunlap, Keith Shearwin, Laura Finzi<\/p><\/td>

\u201cProteins mediating different DNA topologies block RNAP elongation with different efficiency.\u201d<\/p>

Editor\u2019s choice-Journal cover<\/u>.<\/p><\/td>

\u00a0<\/em>FEBS Letters<\/em><\/td>_<\/em><\/td>\u00a0_<\/td>2022<\/td><\/tr>
Jin Qian, David Dunlap, Laura Finzi<\/td>\u201cBasic mechanisms and kinetics of pause-interspersed transcript elongation<\/a>\u201d<\/td>\u00a0<\/em>Nucleic Acids Research<\/i><\/td>49<\/em><\/td>\u00a015-24<\/td>2021<\/td><\/tr>
Jin Qian, Wenxuan Xu, David Dunlap, Laura Finzi<\/td>\u201cSingle-molecule insights into torsion and roadblocks in bacterial transcript elongation\u201d<\/a>

<\/td>		\u00a0<\/em>Transcription<\/em><\/td>12<\/td>\u00a0219-231<\/td>2021<\/td><\/tr>

Zsuzsanna Voros, Yan Yan, David D. Dunlap, Laura Finzi<\/p><\/td>

\u201cProtein-mediated DNA looping enhances roadblocks\u201d<\/td>\u00a0<\/em>Protein Science<\/i><\/td>_<\/em><\/td>\u00a0_<\/td>2017<\/td><\/tr>

S. Ucuncuoglu, K. L. Engel, P. K. Purohit, D. D. Dunlap, D. A. Schneider, Laura Finzi<\/p><\/td>

\u201cDirect characterization of transcription elongation by RNA polymerase I\u201d<\/td>\u00a0<\/em>PLOS One<\/i><\/td>_<\/em><\/td>\u00a0_<\/td>2016<\/td><\/tr><\/tbody><\/table>

Relevant Techniques<\/h3>

Method<\/strong><\/p><\/td>

\u00a0Used for<\/strong><\/p><\/td><\/tr>

AFM<\/p><\/td>

to visualize transcriptional elongation<\/p><\/td><\/tr>

TPM<\/p><\/td>

to monitor the rate of transcriptional elongation and topological changes in the absence of force<\/p><\/td><\/tr>

MTs<\/p><\/td>

to monitor the rate and dynamics of transcriptional elongation and topological changes in the presence of force<\/p><\/td><\/tr>

C-Trap<\/p><\/td>

to monitor the dynamics of transcriptional elongation while simultaneously visualizing the activity of transcription factors<\/p><\/td><\/tr><\/tbody><\/table>

Complete List of Published Work in MyBibliography:<\/h4>

https:\/\/www.ncbi.nlm.nih.gov\/myncbi\/browse\/collection\/40647244\/?sort=date&direction=descending<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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Living organisms thrive, grow and reproduce thanks to a well-regulated transcription program. We wish to understand the physical laws that underlie regulatory mechanisms. This is a multifaceted problem that involves understanding the mechanical properties of DNA in different environments and how such properties affect DNA interaction with proteins, including molecular motors that carry out, or […]<\/p>\n","protected":false},"author":4,"featured_media":382,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"site-sidebar-layout":"no-sidebar","site-content-layout":"","ast-site-content-layout":"default","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":"","ast-breadcrumbs-content":"","ast-featured-img":"","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":""},"categories":[5],"tags":[],"class_list":["post-247","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-research"],"_links":{"self":[{"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/posts\/247","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/types\/post"}],"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=247"}],"version-history":[{"count":0,"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/posts\/247\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/media\/382"}],"wp:attachment":[{"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/media?parent=247"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/categories?post=247"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/tags?post=247"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}