High nucleotide skew palindromic DNA sequences function as replication origins due to their unzipping propensity
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arXiv
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| Main Authors: | , , , |
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| Format: | Preprint |
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2024
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| _version_ | 1866909261578108928 |
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| author | Sahu, Parthasarathi Barik, Sashikanta Ghosh, Koushik Subramanian, Hemachander |
| author_facet | Sahu, Parthasarathi Barik, Sashikanta Ghosh, Koushik Subramanian, Hemachander |
| contents | Locations of DNA replication initiation in prokaryotes, called "origins of replication", are well-characterized. However, a mechanistic understanding of the sequence-dependence of the local unzipping of double-stranded DNA, the first step towards replication initiation, is lacking. Here, utilizing a Markov chain model that was created to address the directional nature of DNA unzipping and replication, we model the sequence dependence of local melting of double-stranded linear DNA segments. We show that generalized palindromic sequences with high nucleotide skews have a low kinetic barrier for local melting near melting temperatures. This allows for such sequences to function as replication origins. We support our claim with evidence for high-skew palindromic sequences within the replication origins of mitochondrial DNA, bacteria, archaea and plasmids. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2407_13260 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | High nucleotide skew palindromic DNA sequences function as replication origins due to their unzipping propensity Sahu, Parthasarathi Barik, Sashikanta Ghosh, Koushik Subramanian, Hemachander Genomics Biomolecules Quantitative Methods Locations of DNA replication initiation in prokaryotes, called "origins of replication", are well-characterized. However, a mechanistic understanding of the sequence-dependence of the local unzipping of double-stranded DNA, the first step towards replication initiation, is lacking. Here, utilizing a Markov chain model that was created to address the directional nature of DNA unzipping and replication, we model the sequence dependence of local melting of double-stranded linear DNA segments. We show that generalized palindromic sequences with high nucleotide skews have a low kinetic barrier for local melting near melting temperatures. This allows for such sequences to function as replication origins. We support our claim with evidence for high-skew palindromic sequences within the replication origins of mitochondrial DNA, bacteria, archaea and plasmids. |
| title | High nucleotide skew palindromic DNA sequences function as replication origins due to their unzipping propensity |
| topic | Genomics Biomolecules Quantitative Methods |
| url | https://arxiv.org/abs/2407.13260 |