title: Is DNA code periodicity only due to CUF-codons usage frequency?
abstract: The triplet code for proteins and functional RNA has been either from the universal pattern of ancient RNA (-H1) [1], with a key role of an uneven codon usage frequency (CUF) in the periodic patterns origination, or a reading frame monitoring device (RFMD -H2) [2- 4]. H1 has lately been upheld [1] but in a single sequence sensitive way [1]. Since H1 and H2 are not mutually exclusive [2, 3, 4], a single sequence-wise sensitive approach by a resonant recognition model (RRM) has become the attempt described in this paper to challenge H1 and H2 in eukaryotes case as a novelty. In the RRM model [5, 6, 7] two bio-molecules interact favorably provided they both obey a common frequency and opposite phases consensus in their delocalized electron energy (DEE-) distributions [5]. Hence it has been possible to learn how well the DEE-s of the mRNA and of the ribosome match each other at 1/3 Hz - that applied to both the original and the CUF preserving randomly shuffled genomic data across the well known Bursét and Guigo collection of 570 coding vertebrates' genes. The matching of RRM patterns reduces to harmonics phase comparison of the relevant DEE-s, a task by a digital phase locked loop (DPLL) [8, 9, and 10]. The DPLL phase control to meet the RRM phase matching case is quantified into a small number of classes to describe the mRNA-ribosome interaction in a categorical way.
authors.affiliation: Biomed. Signals Analysis Lab., L. Rydygier Collegium Medicum, Nicolaus Copernicus Univ. of Torun. zoltm@ieee.org
authors.forename: Mariusz
authors.initials: M
authors.lastname: Zoltowski
mesh_terms: D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D003198:Computer Simulation; D004247:DNA / Q000235:genetics*; D005787:Gene Frequency / Q000235:genetics*; D005815:Genetic Code / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010507:Periodicity; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D003062:Codon; D004247:DNA