Simulation of DNA Supercoil Relaxation. [PDF]
Biophys J, 2016 Several recent single-molecule experiments observe the response of supercoiled DNA to nicking endonucleases and topoisomerases. Typically in these experiments, indirect measurements of supercoil relaxation are obtained by observing the motion of a large micron-sized bead.
Ivenso ID, Lillian TD.
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Supercoil formation in DNA denaturation [PDF]
Physical Review E, 2008 We generalize the Poland-Scheraga (PS) model to the case of a circular DNA, taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we assume that the torsional stress induced by denaturation enforces formation of supercoils whose writhe absorbs the linking number expelled by ...
Alkan Kabakçıoğlu +2 more
openalex +8 more sources
Recognition of DNA Supercoil Handedness during Catenation Catalyzed by Type II Topoisomerases. [PDF]
Biochemistry, 2022 Dalvie ED +3 more
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Telling Your Right Hand from Your Left: The Effects of DNA Supercoil Handedness on the Actions of Type II Topoisomerases. [PDF]
Int J Mol Sci, 2023 Jian JY, Osheroff N.
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DNA sequence encodes the position of DNA supercoils
eLife, 2018 The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural ...
Sung Hyun Kim +5 more
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Epigenetic control of topoisomerase 1 activity presents a cancer vulnerability [PDF]
Nature CommunicationsDNA transactions introduce torsional constraints that pose an inherent risk to genome integrity. While topoisomerase 1 (TOP1) activity is essential for DNA supercoil removal, the aberrant stabilization of TOP1:DNA cleavage complexes (TOP1ccs) can result ...
Tae-Hee Lee +13 more
doaj +2 more sources
Free energy calculations reveal rotating-ratchet mechanism for DNA supercoil relaxation by topoisomerase IB and its inhibition. [PDF]
Biophys J, 2010 Wereszczynski J, Andricioaei I.
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Stemless molecular beacon probes for single-molecule detection of supercoil-induced DNA denaturation. [PDF]
NPJ Biol Phys MechShaheen C +8 more
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Human Smc5/6 recognises transcription-generated positive DNA supercoils. [PDF]
Nat CommunDiman A +5 more
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A multiscale dynamic model of DNA supercoil relaxation by topoisomerase IB. [PDF]
Biophys J, 2011 Lillian TD +4 more
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