A binary representation of the genetic code

Abstract

This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA bases is assigned a unique 2-bit identifier, so that the 64 triplet codons are each indexed by a 6-bit label. The ordering of the bits reflects the hierarchical organization manifested by the DNA replication/repair and tRNA translation systems. In this system, transition and transversion mutations are naturally expressed as binary operations, and the severities of the different point mutations can be analyzed. Using a principal component analysis, it is shown that the physicochemical properties of amino acids related to protein folding also correlate with certain bit positions of their respective labels. Thus, the likelihood for a point mutation to be conservative, and less likely to cause a change in protein functionality, can be estimated.

Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes

“…Correlations with sums and subtractions between any pairs of these six binary values also yield r = 0. Results are identical if one pairs nucleotides according to keto versus amino nucleotides as previously reported [47] , [48] . This means that CDA catches a genetic code dimension that differs from classically recognised codon properties.…”

“…To what extent does CDA represent a dimension of the genetic code that is independent of other dimensions? In this respect, we compare Table 1 with the binary representation of the genetic code [ 47 , therein figure 6], a rather complete 6-bit representation of each codon. It assigns to each codon position two binary values, the first representing the purine-pyrimidine divide, the second value represents whether the nucleotide forms two or three hydrogen interactions when in duplex conformation with an inverse-complementary strand.…”

Visualizing Amino Acid Substitutions in a Physicochemical Vector Space

“…This work builds on previous results, including a principal component analysis (PCA) used to generate the 3D representation in physicochemical space (figure 1), 32 as well as the classification system for DNA mutations. 33 Here, only nonsynonymous missense mutations are considered, and when combining forward and backward changes together, there are (20 x 19)/2 = 190 possible amino acid substitution pairs.…”

Chemical Characterization of Interacting Genes in Few Subnetworks of Alzheimer’s Disease

“…DNA sequences are combinations of four nucleotides A, T, C, G. Depending upon the chemical structures the four bases can form 16 combinations of dual nucleotides along with repeat bases (AG,GA,CT,TC,AC,CA,GT,TG,AT,TA,GC,CG,AA,TT,CC,GG). Depending upon the chemical structure along with repeating DN groups, the dual nucleotides are classified into seven (07) possible classes [10] given in Table 1. According to the definition of central dogma, transcription and translation are the two steps, through which the information in genes flows into proteins.…”