Structural Features of the Nucleotide Sequences of Genomes

Abstract

We propose structural features of genomic DNA, which are essential to generate and to analyze genome. We calculated the appearance frequency of the nucleotides (bases) of throughout the entire genome as a polynucleotide molecule consisting of Adenine (A), Thymine (T), Guanine (G) and Cytosine (C) bases including the coding- and the non-coding regions, primarily in the genomes of Saccharomyces cerevisiae, Escherichia coli, and Homo sapiens. Our results indicate that the base sequences in a single-strand of DNA have the following characteristics: (1) reverse-complement symmetry of 3-9 successive bases, (2) bias and (3) multiple fractality of the distribution of four bases, A, T, G and C depending on the distance, exponentially decreased at short distances and linearly decreased at long distances in double logarithmic plot (power spectrum) of L (the distance of a base to the next base) vs P (L) (the probability of the base-distribution at L). These structural features of a single-strand of DNA can be clearly observed in any genomic DNA, especially observed remarkable in eukaryotic genome. Whereas in the artificial genomes or chromosomes with the same base-numbers, the same base-contents and the same frequencies of 64 triplets, the bias and the linearly-decreased fractality of the distribution of four bases described the above were missing, although the reverse-complement symmetry of the base sequences and the exponentially decreased-fractality of the base distribution were observed.