We investigate DNA stretching during electrophoresis when the mobility abruptly changes. This is a simplified geometry that produces a nonhomogeneous strain rate over the scale of a single molecule. An effective Weissenberg number (Wi) and Deborah number were identified, and the degree of stretching was examined as a function of these two parameters. The system does not undergo a coil-stretch transition. The finite extensibility of the chains only affects the response if the chain is stretched to a significant fraction of the contour length. The wormlike chain shows a characteristic approach to full extension of Wi(-1/2).
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http://dx.doi.org/10.1103/PhysRevE.76.011805 | DOI Listing |
Cell Death Dis
January 2025
Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany.
The transcription factor p63 is expressed in many different isoforms as a result of differential promoter use and splicing. Some of these isoforms have very specific physiological functions in the development and maintenance of epithelial tissues and surveillance of genetic integrity in oocytes. The ASPP family of proteins is involved in modulating the transcriptional activity of the p53 protein family members, including p63.
View Article and Find Full Text PDFCell Rep
January 2025
Molecular Immunology, Justus-Liebig-University Giessen, 35392 Giessen, Germany. Electronic address:
Control of cell proliferation is critical for the lymphocyte life cycle. However, little is known about how stage-specific alterations in cell cycle behavior drive proliferation dynamics during T cell development. Here, we employed in vivo dual-nucleoside pulse labeling combined with the determination of DNA replication over time as well as fluorescent ubiquitination-based cell cycle indicator mice to establish a quantitative high-resolution map of cell cycle kinetics of thymocytes.
View Article and Find Full Text PDFbioRxiv
December 2024
Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA.
Molecular crowding influences DNA mechanics and DNA - protein interactions and is ubiquitous in living cells. Quantifying the effects of molecular crowding on DNA supercoiling is essential to relating experiments to DNA supercoiling. We use single molecule magnetic tweezers to study DNA supercoiling in the presence of dehydrating or crowding co-solutes.
View Article and Find Full Text PDFMethods Mol Biol
December 2024
Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.
Methods Mol Biol
December 2024
Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA.
Homologous recombination (HR) is the principal pathway undertaken by a cell for the error-free repair of DNA double-strand breaks that are frequently encountered by the cell. HR can be initiated at the sites of DNA double-strand breaks by generating long stretches of single-stranded 3' DNA overhang through a process called DNA end resection. In one DNA end resection pathway, this is achieved via the concerted effort of specialized machinery involving the RecQ family helicase BLM, the helicase/endonuclease DNA2, and a single-strand DNA binding protein complex RPA.
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