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Single-Frame, Multiple-Frame and Framing Motifs in Genes

Theoretical Bioinformatics, ICube, CNRS, University of Strasbourg, 300 Boulevard Sébastien Brant, 67400 Illkirch, France
Received: 17 November 2018 / Revised: 24 January 2019 / Accepted: 31 January 2019 / Published: 10 February 2019
We study the distribution of new classes of motifs in genes, a research field that has not been investigated to date. A single-frame motif SF has no trinucleotide in reading frame (frame 0) that occurs in a shifted frame (frame 1 or 2), e.g., the dicodon AAACAA is S F as the trinucleotides AAA and CAA do not occur in a shifted frame. A motif which is not single-frame S F is multiple-frame M F . Several classes of M F motifs are defined and analysed. The distributions of single-frame S F motifs (associated with an unambiguous trinucleotide decoding in the two 5 3 and 3 5 directions) and 5′ unambiguous motifs 5 U (associated with an unambiguous trinucleotide decoding in the 5 3 direction only) are analysed without and with constraints. The constraints studied are: initiation and stop codons, periodic codons { A A A , C C C , G G G , T T T } , antiparallel complementarity and parallel complementarity. Taken together, these results suggest that the complementarity property involved in the antiparallel (DNA double helix, RNA stem) and parallel sequences could also be fundamental for coding genes with an unambiguous trinucleotide decoding in the two 5 3 and 3 5 directions or the 5 3 direction only. Furthermore, the single-frame motifs S F with a property of trinucleotide decoding and the framing motifs F (also called circular code motifs; first introduced by Michel (2012)) with a property of reading frame decoding may have been involved in the early life genes to build the modern genetic code and the extant genes. They could have been involved in the stage without anticodon-amino acid interactions or in the Implicated Site Nucleotides (ISN) of RNA interacting with the amino acids. Finally, the S F and M F dipeptides associated with the S F and M F dicodons, respectively, are studied and their importance for biology and the origin of life discussed. View Full-Text
Keywords: single-frame motifs; multiple-frame motifs; framing motifs; gene coding; antiparallel and parallel sequences; early life genes single-frame motifs; multiple-frame motifs; framing motifs; gene coding; antiparallel and parallel sequences; early life genes
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Michel, C.J. Single-Frame, Multiple-Frame and Framing Motifs in Genes. Life 2019, 9, 18.

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