High Nucleotide Skew Palindromic DNA Sequences Function as Potential Replication Origins due to their Unzipping Propensity.

IF 2.1 3区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Evolution Pub Date : 2024-09-23 DOI:10.1007/s00239-024-10202-y

Parthasarathi Sahu, Sashikanta Barik, Koushik Ghosh, Hemachander Subramanian

引用次数: 0

Abstract

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 potential replication origins. We support our claim with evidence for high-skew palindromic sequences within the replication origins of mitochondrial DNA, bacteria, archaea and plasmids.

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高核苷酸偏斜 Palindromic DNA 序列因其解压缩倾向而成为潜在的复制起源。

原核生物中 DNA 复制的起始位置被称为 "复制起源"，其特征已经非常清楚。然而，人们对复制启动的第一步--双链DNA局部解压缩的序列依赖性缺乏机理上的了解。在这里，我们利用为解决 DNA 解压缩和复制的方向性问题而创建的马尔可夫链模型，模拟了双链线性 DNA 片段局部熔化的序列依赖性。我们的研究表明，具有高核苷酸偏斜的广义回文序列在接近熔化温度时局部熔化的动力学障碍较低。这使得这类序列可以作为潜在的复制起源发挥作用。我们在线粒体 DNA、细菌、古菌和质粒的复制起源中发现了高偏斜的回文序列，从而证明了我们的观点。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Molecular Evolution 生物-进化生物学

CiteScore

5.50

自引率

2.60%

发文量

审稿时长

3 months

期刊介绍： Journal of Molecular Evolution covers experimental, computational, and theoretical work aimed at deciphering features of molecular evolution and the processes bearing on these features, from the initial formation of macromolecular systems through their evolution at the molecular level, the co-evolution of their functions in cellular and organismal systems, and their influence on organismal adaptation, speciation, and ecology. Topics addressed include the evolution of informational macromolecules and their relation to more complex levels of biological organization, including populations and taxa, as well as the molecular basis for the evolution of ecological interactions of species and the use of molecular data to infer fundamental processes in evolutionary ecology. This coverage accommodates such subfields as new genome sequences, comparative structural and functional genomics, population genetics, the molecular evolution of development, the evolution of gene regulation and gene interaction networks, and in vitro evolution of DNA and RNA, molecular evolutionary ecology, and the development of methods and theory that enable molecular evolutionary inference, including but not limited to, phylogenetic methods.