Abstract
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.
Highlights
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
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
We have suggested a superstatistical model that is capable of reproducing the statistical laws that govern the arrangement of nucleotides in the primary sequence of bacterial DNA
Summary
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. A better understanding of the DNA mechanical and thermodynamical properties and their impact on its conformational abilities is essential to reveal many regulatory mechanisms at molecular scale and their reflection in the biological systems performance at macroscopic scale. Considerable progress in both theoretical and experimental biophysics in recent decades led to the design and experimental verification of sophisticated mathematical models capable of describing various DNA structural conformations and their physical properties[1,2]. While as a carrier of genetic information the DNA is often treated as a sequence of consecutively arranged nucleotides, its molecular structure is much more complex including multiple packaging levels www.nature.com/scientificreports/
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