title: Why has nature invented three stop codons of DNA and only one start codon?
abstract: We examine the standard genetic code with three stop codons. Assuming that the synchronization period of length 3 in DNA or RNA is violated during the transcription or translation processes, the probability of reading a frameshifted stop codon is higher than if the code would have only one stop codon. Consequently, the synthesis of RNA or proteins will soon terminate. In this way, cells do not produce undesirable proteins and essentially save energy. This hypothesis is tested on the AT-rich Drosophila genome, where the detection of frameshifted stop codons is even higher than the theoretical value. Using the binomial theorem, we establish the probability of reading a frameshifted stop codon within n steps. Since the genetic code is largely redundant, there is still space for some hidden secondary functions of this code. In particular, because stop codons do not contain cytosine, random C → U and C → T mutations in the third position of codons increase the number of hidden frameshifted stops and simultaneously the same amino acids are coded. This evolutionary advantage is demonstrated on the genomes of several simple species, e.g. Escherichia coli.
authors.affiliation: Institute of Mathematics, Academy of Sciences, Žitná 25, CZ-115 67 Prague 1, Czech Republic. krizek@cesnet.cz
authors.forename: Michal
authors.initials: M
authors.lastname: Křížek
authors.forename: Pavel
authors.initials: P
authors.lastname: Křížek
mesh_terms: D000818:Animals; D018387:Codon, Initiator; D018388:Codon, Terminator; D004247:DNA / Q000235:genetics*; D004330:Drosophila / Q000235:genetics; D016368:Frameshift Mutation; D017344:Genes, Insect / Q000235:genetics; D005815:Genetic Code / Q000235:genetics; D049750:Genome, Insect / Q000235:genetics; D006454:Hemoglobins / Q000235:genetics; D006801:Humans; D012313:RNA / Q000235:genetics; D013045:Species Specificity
chemical_list: D018387:Codon, Initiator; D018388:Codon, Terminator; D006454:Hemoglobins; D012313:RNA; D004247:DNA