Binding Kinetics Oppositely Regulates type II Topoisomerase Relaxation and Decatenation Activities
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| Main Authors: | , , , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866911310830108672 |
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| author | Battaglia, Cleis Conforto, Filippo Fosado, Yair Augusto Gutierrez Newton, Matt Cutts, Erin Michieletto, Davide Valdes, Antonio |
| author_facet | Battaglia, Cleis Conforto, Filippo Fosado, Yair Augusto Gutierrez Newton, Matt Cutts, Erin Michieletto, Davide Valdes, Antonio |
| contents | Type II Topoisomerases (topo II) are critical to simplify genome topology during transcription and replication. They identify topological problems and resolve them by passing a double-stranded DNA segment through a transient break in another segment. The precise mechanisms underpinning topo IIs ability to maintain a topologically simple genome are not fully understood. Here, we investigate how binding kinetics affects the resolution of two distinct forms of topological entanglement: decatenation and torsional relaxation. First, by single-molecule measurements, we quantify how monovalent cation concentration affects the dissociation rate of topo II from DNA. Second, we discover that increasing dissociation rates accelerate decatenation while slowing down relaxation catalytic activities. Finally, by using molecular dynamics simulations, we uncover that this opposite behaviour is due to a trade-off between search of target through facilitated diffusion and processivity of the enzyme in catenated versus supercoiled DNA. Thus, our findings reveal that a modulation of topo II binding kinetics can oppositely regulate its topological simplification activity, and in turn can have a significant impact in vivo. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2512_09141 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Binding Kinetics Oppositely Regulates type II Topoisomerase Relaxation and Decatenation Activities Battaglia, Cleis Conforto, Filippo Fosado, Yair Augusto Gutierrez Newton, Matt Cutts, Erin Michieletto, Davide Valdes, Antonio Biological Physics Soft Condensed Matter Type II Topoisomerases (topo II) are critical to simplify genome topology during transcription and replication. They identify topological problems and resolve them by passing a double-stranded DNA segment through a transient break in another segment. The precise mechanisms underpinning topo IIs ability to maintain a topologically simple genome are not fully understood. Here, we investigate how binding kinetics affects the resolution of two distinct forms of topological entanglement: decatenation and torsional relaxation. First, by single-molecule measurements, we quantify how monovalent cation concentration affects the dissociation rate of topo II from DNA. Second, we discover that increasing dissociation rates accelerate decatenation while slowing down relaxation catalytic activities. Finally, by using molecular dynamics simulations, we uncover that this opposite behaviour is due to a trade-off between search of target through facilitated diffusion and processivity of the enzyme in catenated versus supercoiled DNA. Thus, our findings reveal that a modulation of topo II binding kinetics can oppositely regulate its topological simplification activity, and in turn can have a significant impact in vivo. |
| title | Binding Kinetics Oppositely Regulates type II Topoisomerase Relaxation and Decatenation Activities |
| topic | Biological Physics Soft Condensed Matter |
| url | https://arxiv.org/abs/2512.09141 |