The Combinatorial Fusion Cascade to Generate the Standard Genetic Code

Abstract

Combinatorial fusion cascade was proposed as a transition stage between prebiotic chemistry and early forms of life. The combinatorial fusion cascade consists of three stages: eight initial complimentary pairs of amino acids, four protocodes, and the standard genetic code. The initial complimentary pairs and the protocodes are divided into dominant and recessive entities. The transitions between these stages obey the same combinatorial fusion rules for all amino acids. The combinatorial fusion cascade mathematically describes the codon assignments in the standard genetic code. It explains the availability of amino acids with the even and odd numbers of codons, the appearance of stop codons, inclusion of novel canonical amino acids, exceptional high numbers of codons for amino acids arginine, leucine, and serine, and the temporal order of amino acid inclusion into the genetic code. The temporal order of amino acids within the cascade is congruent with the consensus temporal order previously derived from the similarities between the available hypotheses. The control over the combinatorial fusion cascades would open the road for a novel technology to develop artificial microorganisms.

Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays

“…All codons having U as the second base are associated with the most hydrophobic amino acids, and those having A as the second base are associated with the most hydrophilic amino acids [ 53 , 54 ]. This property is natural for the recently proposed combinatorial fusion cascade (CFC), a hypothetical autocatalytic reaction leading to the formation of the SGC ( Figure S3 ) [ 55 ]. According to the CFC, such a division of amino acids was the first stage in the formation of the genetic code before the appearance of the protocodes, at the level of competing amino acid pairs associated with complementary homo-ribonucleotides.…”

“…The blue letters indicate the fusion rules for the dominant and recessive AAA/UUU- and GGG/CCC-pairs to the protocodes. The red letters indicate the fusion rules for dominant and recessive AU- and GC-protocodes to the SGC (see Section 2.1 ) [ 55 ].…”

Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction

“…One [28] is driven by the need to account for the AARS Class division. The other [115] has the advantage of preserving the ability of the coding table to optimize bidirectional coding because it preserves the codon-anticodon assignments to core and surface amino acids (Figure 3a; reference [49]). Satisfying both requirements is quite difficult.…”