Exploring the benefits of DNA-target search with antenna
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arXiv
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| Auteurs principaux: | , |
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| Format: | Preprint |
| Publié: |
2023
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| _version_ | 1866929328261955584 |
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| author | Hedström, Lucas Lizana, Ludvig |
| author_facet | Hedström, Lucas Lizana, Ludvig |
| contents | The most common gene regulation mechanism is when a protein binds to a regulatory sequence to change RNA transcription. However, these sequences are short relative to the genome length, so finding them poses a challenging search problem. This paper presents two mathematical frameworks capturing different aspects of this problem. First, we study the interplay between diffusional flux through a target where the searching proteins get sequestered on DNA far from the target because of non-specific interactions. From this model, we derive a simple formula for the optimal protein-DNA unbinding rate, maximizing the particle flux. Second, we study how the flux flows through a target on a single antenna with variable length. Here, we identify a non-trivial logarithmic correction to the linear behavior relative to the target size proposed by Smoluchowski's flux formula. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2311_11727 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Exploring the benefits of DNA-target search with antenna Hedström, Lucas Lizana, Ludvig Statistical Mechanics Biological Physics The most common gene regulation mechanism is when a protein binds to a regulatory sequence to change RNA transcription. However, these sequences are short relative to the genome length, so finding them poses a challenging search problem. This paper presents two mathematical frameworks capturing different aspects of this problem. First, we study the interplay between diffusional flux through a target where the searching proteins get sequestered on DNA far from the target because of non-specific interactions. From this model, we derive a simple formula for the optimal protein-DNA unbinding rate, maximizing the particle flux. Second, we study how the flux flows through a target on a single antenna with variable length. Here, we identify a non-trivial logarithmic correction to the linear behavior relative to the target size proposed by Smoluchowski's flux formula. |
| title | Exploring the benefits of DNA-target search with antenna |
| topic | Statistical Mechanics Biological Physics |
| url | https://arxiv.org/abs/2311.11727 |