Biomedical Engineering Research Centre, St. Petersburg Electrotechnical University, St. Petersburg, 197376, Russia.
Molecular Genetics of Microorganisms Lab, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Tatarstan, 420008, Russia.
Sci Rep. 2017 Feb 22;7:43034. doi: 10.1038/srep43034.
Understanding the physical principles that govern the complex DNA structural organization as well as its mechanical and thermodynamical properties is essential for the advancement in both life sciences and genetic engineering. Recently we have discovered that the complex DNA organization is explicitly reflected in the arrangement of nucleotides depicted by the universal power law tailed internucleotide interval distribution that is valid for complete genomes of various prokaryotic and eukaryotic organisms. Here we suggest a superstatistical model that represents a long DNA molecule by a series of consecutive ~150 bp DNA segments with the alternation of the local nucleotide composition between segments exhibiting long-range correlations. We show that the superstatistical model and the corresponding DNA generation algorithm explicitly reproduce the laws governing the empirical nucleotide arrangement properties of the DNA sequences for various global GC contents and optimal living temperatures. Finally, we discuss the relevance of our model in terms of the DNA mechanical properties. As an outlook, we focus on finding the DNA sequences that encode a given protein while simultaneously reproducing the nucleotide arrangement laws observed from empirical genomes, that may be of interest in the optimization of genetic engineering of long DNA molecules.
理解控制复杂 DNA 结构组织以及其力学和热力学性质的物理原理，对于生命科学和基因工程的发展至关重要。最近，我们发现复杂的 DNA 组织明确反映在核苷酸排列中，这由普遍的幂律尾部核苷酸间隔分布所描绘，该分布适用于各种原核和真核生物的完整基因组。在这里，我们提出了一个超统计模型，该模型通过一系列连续的约 150bp 的 DNA 片段来表示长 DNA 分子，片段之间的局部核苷酸组成交替出现，表现出长程相关性。我们表明，超统计模型和相应的 DNA 生成算法明确地再现了各种全局 GC 含量和最佳生存温度下 DNA 序列的经验核苷酸排列性质的规律。最后，我们根据模型的 DNA 力学性质来讨论其相关性。展望未来，我们专注于在给定蛋白质编码的同时找到 DNA 序列，同时再现从经验基因组中观察到的核苷酸排列规律，这可能对长 DNA 分子的基因工程优化具有重要意义。
