The rules of variation: Amino acid exchange according to the rotating circular genetic code

Abstract

General guidelines for the molecular basis of functional variation are presented while focused on the rotating circular genetic code and allowable exchanges that make it resistant to genetic diseases under normal conditions. The rules of variation, bioinformatics aids for preventive medicine, are: (1) same position in the four quadrants for hydrophobic codons, (2) same or contiguous position in two quadrants for synonymous or related codons, and (3) same quadrant for equivalent codons. To preserve protein function, amino acid exchange according to the first rule takes into account the positional homology of essential hydrophobic amino acids with every codon with a central uracil in the four quadrants, the second rule includes codons for identical, acidic, or their amidic amino acids present in two quadrants, and the third rule, the smaller, aromatic, stop codons, and basic amino acids, each in proximity within a 90 degree angle. I also define codifying genes and palindromati, CTCGTGCCGAATTCGGCACGAG.

Genetic code: Chemical Distinctions of Protein Amino Acids

“…All the present arrangements and regularities are an addition to the previously revealed systems and arrangements of protein amino acids (as constituents of GC) in which chemical distinctions and classifications are accompanied by arithmetical and algebraic regularities, both in our previous works and in the works of other authors (Rumer, 1966; Kyte & Doolittle,1982; Doolittle,1985; Sukhodolets,1985; Leunissen and De Jong,1986;Taylor & Coates, 1989; Koruga,1992;Shcherbak, 1994; Damjanovic, 1998;Dragovich and Dragovich, 2006;Négadi, 2009;Castro-Chavez, 2010; Mišic, 2011;Petoukhov, 2016;Dragovich et al, 2017).…”

“…4 "With insight into the results ... one is forced to propose a hypothesis (for further researches) that here, there really is a kind of intelligent design; not the original intelligent design, dealing with the question -intelligent design or evolution, which is rightly criticized .... Here, there could be such an intelligent design, which we could call "Spontaneous Intelligent Design" SPID) that is consistent with that design which was presented by F. Castro-Chavez (2010), and is also in accordance with the Darwinism" (Rakočević, 2015, footnote 47) [Additional note: The evidence that Darwin tacitly advocates the idea of intelligent design, learns from the insight that his only illustration (Diagram) (Rakočević, 1994;.] 5 These pairs are exceptions also in the basic chemical characteristic.…”

Escaping the Cut by Restriction Enzymes Through Single-Strand Self-Annealing of Host-Edited 12-bp and Longer Synthetic Palindromes

“…The 22-bp palindromic sequence 5¢ CTCGTGCCGAAT TCGGCACGAG 3¢ was reported earlier by the author of this article as a sequence contaminant (Castro-Chavez, 2004, 2010, and is illustrated in Figure 2C.…”

“…Finally, by comparing the translation from codons to proteins with the rotating genetic code (Castro-Chavez, 2010, 2011, the translated palindromes were detected as contaminants. Exemplified in Table 2 is the seriousness of the contamination by EcoRI adaptors and linkers if they are translated as being part of a human exon or protein.…”

“…Palindromati is a laboratory artifact produced by a biological host (yeast or bacteria) interacting with a vector equipped with adaptors. Through host-vector interactions, those adaptors are generating either full or partial palindromes or palindromic sequences capable of single-strand self-annealing that are preventing them from being degraded by restriction enzymes such as the active dimer formed by EcoRI (Castro-Chavez, 2010, 2011. The normal digestion of EcoRI is represented in Figure 2A.…”