Particular and General Limitations in Gene Coding and Synonymous Recoding of Genes

Pub Date : 2024-07-09 DOI:10.3103/s0891416824700058
E. P. Kharchenko
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Abstract

In the intensively developing field of synthetic biology, synonymous gene recoding is a leading method, which is not without drawbacks in its use. There are natural limitations in the use of codons in genes. Computer analysis in 30 genes of viruses, bacteria, archaea, and human beings was used to study the nucleotide composition, the translational code of the proteins encoded by them, and the composition of dinucleotides, dicodons, and tricodons. To identify limitations in gene coding, sequences of quantitative indicators of codons (complementarity indices (CIs) and dimension indices) were used. For each gene, limitations (particular) in the nucleotide composition, the translational code, and the composition of dinucleotides and dicodons were identified. A general limitation in gene coding is that the difference in the CIs of neighboring tricodons read with a frame shift of one codon, as happens when mRNA is translated on ribosomes, was no more than 2 in the vast majority of tricodons. Since in genes each codon is included in three sequentially read tricodons, with the exception of the first and last three codons, the CI of each codon is associated with the CIs of the two preceding and two subsequent codons. This leads to the recognition of the existence of a continuum of the codon connectivity in genes based on their CI values.

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基因编码和基因同义重编码的特殊和一般限制
在合成生物学领域蓬勃发展的过程中,同义基因重编码是一种主要的方法,但在使用过程中也并非没有缺点。基因中密码子的使用存在天然的局限性。通过对病毒、细菌、古生物和人类的 30 个基因进行计算机分析,研究了这些基因的核苷酸组成、所编码蛋白质的翻译密码,以及二核苷酸、二密码子和三密码子的组成。为了确定基因编码的局限性,使用了密码子定量指标序列(互补性指数(CI)和维度指数)。针对每个基因,确定了核苷酸组成、翻译密码以及二核苷酸和二密码子组成中的限制(特定)。基因编码的一个普遍限制是,在绝大多数三核苷酸中,相邻三核苷酸的 CIs 差值不超过 2,而当 mRNA 在核糖体上翻译时,相邻三核苷酸的 CIs 差值为一个密码子的帧移位。由于基因中的每个密码子都包含在三个顺序读取的三密码子中,除了第一个和最后一个密码子,每个密码子的 CI 都与前两个和后两个密码子的 CI 相关联。这就使人们认识到,根据密码子的 CI 值,基因中存在连续的密码子连接。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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