Abstract
The four nucleotides (bases), A, T (U), G and C in small genomes, virus DNA/RNA, organelle and plastid genomes were also arranged sophisticatedly in the structural features in a single-strand with 1) reverse-complement symmetry of base or base sequences, 2) bias of four bases, 3) multiple fractality of the distribution of each four bases depending on the distance 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), although their genomes were composed of low numbers of the four bases, and the base-symmetry was rather lower than the prokaryotic-and the eukaryotic cells. In the case of the genomic DNA composed of less than 10,000 nt, it was better than to be partitioned at 10 of the L-value, and the structural features for the biologically active genomic DNA were observed as the large genomes. As the results, the base sequences of the genomic DNA including the genomic-RNA might be universal in all genomes. In addition, the relationship between the structural features of the genome and the biological complexity was discussed.
Highlights
Watson and Crick deduced that DNA had a doublehelical structure with complementary and anti-paralleled strands [1] based on the equal amounts of adenine (A) and thymine (T), and guanine (G) and cytosine (C) by Chargaff [2], and the X-ray diffraction patterns of DNA fibers by R
The four nucleotides, A, T (U), G and C in small genomes, virus DNA/RNA, organelle and plastid genomes were arranged sophisticatedly in the structural features in a single-strand with 1) reversecomplement symmetry of base or base sequences, 2) bias of four bases, 3) multiple fractality of the distribution of each four bases depending on the distance in double logarithmic plot of L vs. P (L), their genomes were composed of low numbers of the four bases, and the base-symmetry was rather lower than the prokaryotic- and the eukaryotic cells
The genome base sequences of many organisms described below have been determined, and an artificial bacterial genome (582,970 bp) was chemically synthesized based on Mycoplasma genitalium [6], partial unreadable regions still remained in each genome
Summary
Watson and Crick deduced that DNA had a doublehelical structure with complementary and anti-paralleled strands [1] based on the equal amounts of adenine (A) and thymine (T), and guanine (G) and cytosine (C) by Chargaff [2], and the X-ray diffraction patterns of DNA fibers by R. Chargaff and co-workers observed that a single-strand of Bacillus subtilis DNA had the same amount of A + T and G + C ([5]; Chargaff’s second parity-rule, 1968). The genome base sequences of many organisms described below have been determined, and an artificial bacterial genome (582,970 bp) was chemically synthesized based on Mycoplasma genitalium [6], partial unreadable regions still remained in each genome. The structural analysis of the DNA based on the entire genome base sequence was necessary to understand living organisms. We had to characterize the structural features of genomic DNA
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