DNA end tethering through break-induced DNA--protein condensation
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| Format: | Preprint |
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2026
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| _version_ | 1866913159914192896 |
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| author | Das, Rakesh Mascarenhas, Tarun Chappidi, Nagaraja Alberti, Simon Jülicher, Frank |
| author_facet | Das, Rakesh Mascarenhas, Tarun Chappidi, Nagaraja Alberti, Simon Jülicher, Frank |
| contents | Cells deploy robust mechanisms to repair DNA damage, safeguarding genomic stability and cellular health, but the physical principles underlying these processes remain incompletely understood. Experiments show \emph{in vitro} that upon a DNA double-strand break, a DNA--protein condensate can tether the broken DNA ends before they disperse away, a critical step for subsequent repair biochemistry. However, it remains puzzling how such condensation reliably achieves spatiotemporal localization at the break site and captures both broken ends despite intrinsic stochasticity. Here, we propose that broken DNA ends can trigger a conversion of proteins from a soluble state to a condensate-competent state. Combining this idea with Brownian dynamics simulations and theory, we propose a physical mechanism for reliable DNA-end tethering. Simulations show that such break-induced conversion can drive local DNA--protein condensation with two possible outcomes: successful or failed tethering. To rationalize this, we construct an effective free energy landscape, identify the corresponding stationary states, and demonstrate that tethering is governed by a kinetic competition between polymer relaxation and condensation dynamics. Together, our study shows that DNA end-dependent conversion, coupled with DNA--protein condensation, can reliably tether broken DNA ends. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2605_24987 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | DNA end tethering through break-induced DNA--protein condensation Das, Rakesh Mascarenhas, Tarun Chappidi, Nagaraja Alberti, Simon Jülicher, Frank Biological Physics Soft Condensed Matter Cells deploy robust mechanisms to repair DNA damage, safeguarding genomic stability and cellular health, but the physical principles underlying these processes remain incompletely understood. Experiments show \emph{in vitro} that upon a DNA double-strand break, a DNA--protein condensate can tether the broken DNA ends before they disperse away, a critical step for subsequent repair biochemistry. However, it remains puzzling how such condensation reliably achieves spatiotemporal localization at the break site and captures both broken ends despite intrinsic stochasticity. Here, we propose that broken DNA ends can trigger a conversion of proteins from a soluble state to a condensate-competent state. Combining this idea with Brownian dynamics simulations and theory, we propose a physical mechanism for reliable DNA-end tethering. Simulations show that such break-induced conversion can drive local DNA--protein condensation with two possible outcomes: successful or failed tethering. To rationalize this, we construct an effective free energy landscape, identify the corresponding stationary states, and demonstrate that tethering is governed by a kinetic competition between polymer relaxation and condensation dynamics. Together, our study shows that DNA end-dependent conversion, coupled with DNA--protein condensation, can reliably tether broken DNA ends. |
| title | DNA end tethering through break-induced DNA--protein condensation |
| topic | Biological Physics Soft Condensed Matter |
| url | https://arxiv.org/abs/2605.24987 |