title: Fundamental role of start/stop regulators in whole DNA and new trinucleotide classification.
abstract: The origin and logic of genetic code are two of greatest mysteries of life sciences. Analyzing DNA sequences we showed that the start/stop trinucleotides have broader importance than just marking start and stop of exons in coding DNA. On this basis, here we introduced new classification of trinucleotides and showed that all A+T rich trinucleotides consisting of three different nucleotides arise from start-ATG, stop-TGA and stop-TAG using their complement, reverse complement and reverse transformations. Due to the same transformations during generations of crossing-over they can switch from one form to the other. By direct process the start-ATG and stop-TAG can irreversibly transform into stop-TAA. By transformation into A+T rich trinucleotides and 16/32 C+G rich they can lose the start/stop function and take the role of a sense codon in reversible way. The remaining 16 C+G trinucleotides cannot directly transform into start/stop trinucleotides and thus remain a firm skeleton for structuring the C+G rich DNA. We showed that start/stops strongly enrich the A+T rich noncoding DNA through frequently extended forms. From the evolutionary viewpoint the start/stops are chief creators of prevailing A+T rich noncoding DNA, and of more stable coding DNA. We propose that start/stops have basic role as "seeds" in trinucleotide evolution of noncoding and coding sequences and lead to asymmetry between A+T and C+G rich DNA. By dynamical transformations during evolution they enabled pronounced phylogenetic broadness, keeping the regulator function.
authors.affiliation: Faculty of Science, University of Zagreb, Bijenička 32, 10000 Zagreb, Croatia.
authors.forename: Marija
authors.initials: M
authors.lastname: Rosandić
authors.forename: Vladimir
authors.initials: V
authors.lastname: Paar
authors.forename: Matko
authors.initials: M
authors.lastname: Glunčić
mesh_terms: D001483:Base Sequence / Q000502:physiology; D003062:Codon / Q000145:classification* / Q000235:genetics; D018387:Codon, Initiator / Q000235:genetics*; D018388:Codon, Terminator / Q000235:genetics*; D004247:DNA / Q000235:genetics; D019143:Evolution, Molecular; D005580:Fossils; D005815:Genetic Code / Q000502:physiology*; D006801:Humans; D008969:Molecular Sequence Data; D012045:Regulatory Sequences, Nucleic Acid / Q000502:physiology*; D012441:Saccharomyces cerevisiae / Q000235:genetics
chemical_list: D003062:Codon; D018387:Codon, Initiator; D018388:Codon, Terminator; D004247:DNA
keywords: CLT; Genetic code; HOR; Noncoding DNA; Regulators; Start trinucleotide; Stop trinucleotides; TNT; Trinucleotide classification; codon like trinucleotide; higher order repeat; trinucleotide