Castro-Chavez Fernando
Neuroquantology. 2011 Dec;9(4). doi: 10.14704/nq.2011.9.4.500.
My previous theoretical research shows that the rotating circular genetic code is a viable tool to make easier to distinguish the rules of variation applied to the amino acid exchange; it presents a precise and positional bio-mathematical balance of codons, according to the amino acids they codify. Here, I demonstrate that when using the conventional or classic circular genetic code, a clearer pattern for the human codon usage per amino acid and per genome emerges. The most used human codons per amino acid were the ones ending with the three hydrogen bond nucleotides: C for 12 amino acids and G for the remaining 8, plus one codon for arginine ending in A that was used approximately with the same frequency than the one ending in G for this same amino acid (plus *). The most used codons in man fall almost all the time at the rightmost position, clockwise, ending either in C or in G within the circular genetic code. The human codon usage per genome is compared to other organisms such as fruit flies (Drosophila melanogaster), squid (Loligo pealei), and many others. The biosemiotic codon usage of each genomic population or 'Theme' is equated to a 'molecular language'. The C/U choice or difference, and the G/A difference in the third nucleotide of the most used codons per amino acid are illustrated by comparing the most used codons per genome in humans and squids. The human distribution in the third position of most used codons is a 12-8-2, C-G-A, nucleotide ending signature, while the squid distribution in the third position of most used codons was an odd, or uneven, distribution in the third position of its most used codons: 13-6-3, U-A-G, as its nucleotide ending signature. These findings may help to design computational tools to compare human genomes, to determine the exchangeability between compatible codons and amino acids, and for the early detection of incompatible changes leading to hereditary diseases.
我之前的理论研究表明，旋转的圆形遗传密码是一种可行的工具，能更轻松地辨别应用于氨基酸交换的变异规则；根据所编码的氨基酸，它呈现出密码子精确的位置生物数学平衡。在此，我证明，当使用传统或经典的圆形遗传密码时，每种氨基酸和每个基因组的人类密码子使用情况会呈现出更清晰的模式。每种氨基酸最常用的人类密码子是以三个氢键核苷酸结尾的那些：12种氨基酸以C结尾，其余8种以G结尾，加上一个以A结尾的精氨酸密码子，其使用频率与该氨基酸以G结尾的密码子大致相同（加上*）。人类最常用的密码子几乎总是在圆形遗传密码中顺时针方向的最右侧位置，以C或G结尾。将每个基因组的人类密码子使用情况与其他生物进行比较，如果蝇（黑腹果蝇）、鱿鱼（佩氏枪乌贼）等。每个基因组群体或“主题”的生物符号学密码子使用情况等同于一种“分子语言”。通过比较人类和鱿鱼每个基因组中最常用的密码子，说明了每种氨基酸最常用密码子第三位的C/U选择或差异以及G/A差异。人类最常用密码子第三位的分布是12 - 8 - 2，即C - G - A核苷酸结尾特征，而鱿鱼最常用密码子第三位的分布在其最常用密码子的第三位是奇数或不均匀分布：13 - 6 - 3，即U - A - G作为其核苷酸结尾特征。这些发现可能有助于设计计算工具来比较人类基因组，确定兼容密码子和氨基酸之间的可交换性，以及早期检测导致遗传疾病的不兼容变化。
