Literature DB >> 18002222

Is DNA code periodicity only due to CUF-codons usage frequency?

Mariusz Zoltowski1.   

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.

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Year:  2007        PMID: 18002222     DOI: 10.1109/IEMBS.2007.4352556

Source DB:  PubMed          Journal:  Annu Int Conf IEEE Eng Med Biol Soc        ISSN: 2375-7477


  3 in total

1.  An approach for searching insertions in bacterial genes leading to the phase shift of triplet periodicity.

Authors:  Maria A Korotkova; Nikolay A Kudryashov; Eugene V Korotkov
Journal:  Genomics Proteomics Bioinformatics       Date:  2011-10       Impact factor: 7.691

2.  [Chromosomal localization and molecular organization of human genomic fragment containing TNF/LT locus in transgenic mice].

Authors:  A R Galimov; A A Kruglov; N L Bol'sheva; O Iu Iurkevich; D Ia Lipin'sh; I A Mufazalov; D V Kuprash; S A Nedospasov
Journal:  Mol Biol (Mosk)       Date:  2008 Jul-Aug

3.  Using triplet periodicity of nucleotide sequences for finding potential reading frame shifts in genes.

Authors:  F E Frenkel; E V Korotkov
Journal:  DNA Res       Date:  2009-03-03       Impact factor: 4.458

  3 in total

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