title: Trinucleotide's quadruplet symmetries and natural symmetry law of DNA creation ensuing Chargaff's second parity rule.
abstract: For almost 50 years the conclusive explanation of Chargaff's second parity rule (CSPR), the equality of frequencies of nucleotides A=T and C=G or the equality of direct and reverse complement trinucleotides in the same DNA strand, has not been determined yet. Here, we relate CSPR to the interstrand mirror symmetry in 20 symbolic quadruplets of trinucleotides (direct, reverse complement, complement, and reverse) mapped to double-stranded genome. The symmetries of Q-box corresponding to quadruplets can be obtained as a consequence of Watson-Crick base pairing and CSPR together. Alternatively, assuming Natural symmetry law for DNA creation that each trinucleotide in one strand of DNA must simultaneously appear also in the opposite strand automatically leads to Q-box direct-reverse mirror symmetry which in conjunction with Watson-Crick base pairing generates CSPR. We demonstrate quadruplet's symmetries in chromosomes of wide range of organisms, from Escherichia coli to Neanderthal and human genomes, introducing novel quadruplet-frequency histograms and 3D-diagrams with combined interstrand frequencies. These "landscapes" are mutually similar in all mammals, including extinct Neanderthals, and somewhat different in most of older species. In human chromosomes 1-12, and X, Y the "landscapes" are almost identical and slightly different in the remaining smaller and telocentric chromosomes. Quadruplet frequencies could provide a new robust tool for characterization and classification of genomes and their evolutionary trajectories.
authors.affiliation: a Croatian Academy of Sciences and Arts, HAZU, Bioinformatics and Biological Physics , Zrinski trg 11, 10000 Zagreb , Croatia.
authors.forename: Marija
authors.initials: M
authors.lastname: Rosandić
authors.affiliation: b Faculty of Science , University of Zagreb , Bijenicka 32, 10000 Zagreb , Croatia.
authors.forename: Ines
authors.initials: I
authors.lastname: Vlahović
authors.affiliation: b Faculty of Science , University of Zagreb , Bijenicka 32, 10000 Zagreb , Croatia.
authors.forename: Matko
authors.initials: M
authors.lastname: Glunčić
authors.affiliation: a Croatian Academy of Sciences and Arts, HAZU, Bioinformatics and Biological Physics , Zrinski trg 11, 10000 Zagreb , Croatia.|b Faculty of Science , University of Zagreb , Bijenicka 32, 10000 Zagreb , Croatia.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Paar
mesh_terms: D000818:Animals; D001482:Base Composition; D002874:Chromosome Mapping; D003062:Codon; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D019143:Evolution, Molecular; D054856:G-Quadruplexes; D016678:Genome; D023281:Genomics; D006801:Humans; D008957:Models, Genetic; D009711:Nucleotides; D018911:Trinucleotide Repeats
chemical_list: D003062:Codon; D009711:Nucleotides; D004247:DNA
keywords: Chargaff’s second parity rule; DNA symmetries; Neanderthal genome; human genome; quadruplets of trinucleotides; trinucleotide frequencies