DNA Mechanics and Gene Expression

Presentations

• Laura Finzi

  ORAL · Invited

  March 19, 2025, 11:00 AM – March 19, 2025, 11:36 AM

  Presenters

  • Laura Finzi

    Clemson University

  Authors

  • Laura Finzi

    Clemson University

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• DNA duplex stabilization by neighboring elements through nonlocal interactions

  ORAL

  March 19, 2025, 11:36 AM – March 19, 2025, 11:48 AM

  Presenters

  • Harold D Kim

    Georgia Institute of Technology

  Authors

  • Harold D Kim

    Georgia Institute of Technology

  • Alec Cook

    GT Physics, Georgia Tech

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• Visualizing DNA Minicircles for Poloidal Bias

  ORAL

  March 19, 2025, 11:48 AM – March 19, 2025, 12:00 PM

  Presenters

  • Tony Lemos

    Georgia Institute of Technology

  Authors

  • Tony Lemos

    Georgia Institute of Technology

  • Harold D Kim

    Georgia Institute of Technology

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• Understanding How Transient Interactions Shape the Affinity of NF-κB Transcription Factor for DNA via Molecular Dynamics Simulations and Machine Learning

  ORAL

  March 19, 2025, 12:00 PM – March 19, 2025, 12:12 PM

  Publication: Tianjie Li, Shandy Shahabi, Tapan Biswas, Oleg V Tsodikov, Wenfei Pan, De-Bin Huang, Vivien Ya-Fan Wang, Yi Wang, and Gourisankar Ghosh. "Transient interactions modulate the affinity of NF-κB transcription factors for DNA". Proceedings of the National Academy of Sciences. 121.23 (2024), pp. e2405555121. DOI: 10.1073/pnas.2405555121.

  Presenters

  • Tianjie Li

    The Chinese University of Hong Kong

  Authors

  • Tianjie Li

    The Chinese University of Hong Kong

  • Yi Wang

    Chinese University of Hong Kong

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• How to Find Targets That Are Always Hidden: The Story of Nucleosome-Covered DNA and Pioneer Transcription Factors

  ORAL · Invited

  March 19, 2025, 12:12 PM – March 19, 2025, 12:48 PM

  Publication: 1) Nucleosome Breathing Facilitates the Search for Hidden DNA Sites by Pioneer Transcription Factors, (A. Mondal, C. Felipe, and A.B. Kolomeisky), J. Phys. Chem. Lett. 14, 4096-4103 (2023).<br>2) Role of Nucleosome Sliding in the Protein Target Search for Covered DNA Sites, (A. Mondal and A.B. Kolomeisky), J. Phys. Chem. Lett. 14, 7073-7082 (2023).<br>3) How Pioneer Transcription Factors Search for Target Sites on Nucleosomal DNA. (C. Felipe, J. Shin and A.B. Kolomeisky), J. Phys. Chem. B 126, 4061-4068 (2022).

  Presenters

  • Anatoly B Kolomeisky

    Rice University

  Authors

  • Anatoly B Kolomeisky

    Rice University

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• Investigating the bent states of dsDNA defects with nunchucks

  ORAL

  March 19, 2025, 12:48 PM – March 19, 2025, 1:00 PM

  Presenters

  • Ruiyao Liu

    University of California, Santa Barbara

  Authors

  • Ruiyao Liu

    University of California, Santa Barbara

  • Xinyue A Cai

    University of California, Santa Barbara

  • Deborah K Fygenson

    University of California, Santa Barbara

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• Collective coordinates and facilitated translocation of human mitochondrial RNA polymerase (POLRMT) translocation from atomic simulations

  ORAL

  March 19, 2025, 1:00 PM – March 19, 2025, 1:12 PM

  Presenters

  • Shannon J McElhenney

    University of California, Irvine

  Authors

  • Shannon J McElhenney

    University of California, Irvine

  • Jin Yu

    University of California, Irvine

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• Biophysical model explains sequence-specific variation in transcriptional error rates

  ORAL

  March 19, 2025, 1:12 PM – March 19, 2025, 1:24 PM

  Presenters

  • Tripti Midha

    Rice University

  Authors

  • Tripti Midha

    Rice University

  • Anatoly B Kolomeisky

    Rice University

  • Oleg A Igoshin

    Rice Univ

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• Statistical Mechanical Model of the B- to Z-DNAStructural Transition

  ORAL

  March 19, 2025, 1:24 PM – March 19, 2025, 1:36 PM

  Publication: Planned paper in biophysical journal with same title.

  Presenters

  • Zach Montgomerie

    Stanford University

  Authors

  • Zach Montgomerie

    Stanford University

  • Jin Qian

    Emory University

  • David D Dunlap

    Clemson University

  • Laura Finzi

    Clemson University

  • Andrew J Spakowitz

    Stanford University

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• Transcriptional bursting kinetics provide insights into the mechanisms governing Interferon-mediated transcriptional memory

  ORAL

  March 19, 2025, 1:36 PM – March 19, 2025, 1:48 PM

  Publication: We plan to submit the manuscript highlighting this work in the coming months titled: "Inferring bursting kinetics of GBP5 using the generalized two-state model fed by single molecular imaging"

  Presenters

  • Shaswata Roy

    Purdue University

  Authors

  • Shaswata Roy

    Purdue University

  • Jing Liu

    Purdue University

  • Clayton Seitz

    Indiana University

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• Crowder-induced compaction of stretched DNA

  ORAL

  March 19, 2025, 1:48 PM – March 19, 2025, 2:00 PM

  Publication: Manuscript in preparation

  Presenters

  • Laura Finzi

    Clemson University

  Authors

  • Laura Finzi

    Clemson University

  • Jin Qian

    NIH

  • Narendar Kolimi

    Clemson University

  • Quentin Chaboche

    IFOM

  • David D Dunlap

    Clemson University

  • Vittore Scolari

    Institute Marie Curie

  • Marco Cosentino-Lagomarsino

    IFOM

  View abstract →