{"id":249,"date":"2024-10-21T20:55:08","date_gmt":"2024-10-22T00:55:08","guid":{"rendered":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/?p=249"},"modified":"2026-02-10T16:36:59","modified_gmt":"2026-02-10T21:36:59","slug":"methods","status":"publish","type":"post","link":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/methods\/","title":{"rendered":"Methods"},"content":{"rendered":"\t\t
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We continuously devise new methods and optimization protocols to improve performance and sensitivity.
Below are the publications that describe these advances for each specific approach.<\/p>\n

Tethered Particle Microscopy:<\/h4>\n
    \n
  1. Qian J, Collette D, Finzi L, Dunlap D. Detecting DNA Loops Using Tethered Particle Motion. Methods in Molecular Biology (Clifton, N.J.). 2024; 2694:451-466. PubMed PMID: 37824017; DOI: 10.1007\/978-1-0716-3377-9_21
    <\/a><\/li>\n
  2. Laura Finzi and David Dunlap. The tethered particle motion and magnetic tweezer techniques: an introduction and some applications. Proceedings of the International School of Physics \u201cEnrico Fermi\u201d, Multimodal and Nanoscale Optical Microscopy, course 210, 2022.<\/li>\n
  3. Wenxuan Xu, David Dunlap and Laura Finzi. Tethered Particle Microscopy. Encyclopedia of Biophysics, European Biophysical Societies’ Association (EBSA), 2021. DOI: 10.1007\/978-3-642-35943-9_489-1
    <\/a><\/li>\n
  4. Daniel T. Kovari, Yan Yan, Laura Finzi and David Dunlap. Tethered Particle Motion: an easy technique for probing DNA topology and interactions with transcription factors. Methods in Molecular Biology, vol 1665, 2018.<\/li>\n
  5. Suleyman Ucuncuoglu et al. Multiplexed, tethered particle microscopy for studies of DNA-enzyme dynamics. Methods in Enzymology, 2016.<\/li>\n
  6. Sandip Kumar et al. Enhanced Tether Particle Motion Analysis Reveals Viscous Effects. Biophysical Journal, 106(2):399\u2013409, 2014.<\/li>\n
  7. David D. Dunlap et al. Probing DNA topology with Tethered Particle Motion. Methods in Molecular Biology, 2011.<\/li>\n
  8. C. Manzo and L. Finzi. Quantitative analysis of DNA looping kinetics. Methods in Enzymology, 2010.<\/li>\n
  9. John F. Beausang et al. DNA Looping Kinetics Analysed Using Diffusive Hidden Markov Method Model. Biophys J., 2007.<\/li>\n
  10. P. Nelson et al. Tethered Particle Motion as a Diagnostic of DNA Tether Length. J. Phys. Chem. B, 2006.<\/li>\n
  11. E. Consoli et al. Diffusion of phosphorylated and non-phosphorylated LHCII. EMBO Reports, 2005.<\/li>\n<\/ol>\n

    Magnetic Tweezer method:<\/h4>\n
      \n
    1. Laura Finzi and David Dunlap. The tethered particle motion and magnetic tweezer techniques. Enrico Fermi School, 2022.<\/li>\n
    2. Joe Piccolo et al. Force spectroscopy with electromagnetic tweezers. Journal of Applied Physics, 2021.<\/li>\n
    3. Daniel T. Kovari et al. Model-free 3D localization. Optics Express, 2019.<\/li>\n
    4. Sachin Goyal et al. Stretching DNA to quantify non-specific binding. PRE, 2012.<\/li>\n
    5. Qing Shao et al. Physiological salt levels favor writhe. Macromolecules, 2012.<\/li>\n<\/ol>\n

      Atomic Force Microscopy method:<\/h4>\n
        \n
      1. Ning Gao et al. Purification of Bacteriophage Lambda Repressor. Protein Expression and Purification, 2013.<\/li>\n
      2. Marta A. Mendes et al. MADS-domain transcription factor looping. Plant Cell, 2013.<\/li>\n
      3. Haowei Wang et al. Single molecule analysis of DNA wrapping. Nucleic Acids Research, 2013.<\/li>\n
      4. H. Wang et al. AFM studies of CI oligomers. Curr. Pharmaceutical Biotechnology, 2009.<\/li>\n
      5. G. Lia et al. ATP-dependent looping of DNA by ISWI. J. Biophotonics, 2008.<\/li>\n
      6. M. Podest\u00e0 et al. Positively charged surfaces increase DNA flexibility. Biophys J., 2005.<\/li>\n
      7. A. Podest\u00e0 et al. Atomic Force Microscopy studies of DNA. Journal of Microscopy, 2004.<\/li>\n<\/ol>\n

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

        https:\/\/www.ncbi.nlm.nih.gov\/myncbi\/browse\/collection\/40647244\/?sort=date&direction=descending
        <\/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":"

        We continuously devise new methods and optimization protocols to improve performance and sensitivity.Below are the publications that describe these advances for each specific approach. Tethered Particle Microscopy: Qian J, Collette D, Finzi L, Dunlap D. Detecting DNA Loops Using Tethered Particle Motion. Methods in Molecular Biology (Clifton, N.J.). 2024; 2694:451-466. PubMed PMID: 37824017; DOI: 10.1007\/978-1-0716-3377-9_21 Laura […]<\/p>\n","protected":false},"author":4,"featured_media":383,"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-249","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\/249","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=249"}],"version-history":[{"count":0,"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/posts\/249\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/media\/383"}],"wp:attachment":[{"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/media?parent=249"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/categories?post=249"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/finzi-dunlap\/wp-json\/wp\/v2\/tags?post=249"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}