BACKGROUND Theoretical minimal RNA rings code by design over the shortest length once for each of the 20 amino acids, a start and a stop codon, and form stem-loop hairpins. This defines at most 25 RNA rings of 22 nucleotides. As a group, RNA rings mimick numerous prebiotic and early life biomolecular properties: tRNAs, deamination gradients and replication origins, emergence of codon preferences for the natural circular code, and contents of early protein coding genes. These properties result from the RNA ring's in silico design, based mainly on coding nonredundancy among overlapping translation frames, as the genetic code's codon-amino acid assignments determine. RNA rings resemble ancestral tRNAs, defining RNA ring anticodons and corresponding cognate amino acids. Surprisingly, all examined RNA ring properties coevolve with genetic code integration ranks of RNA ring cognates, as if RNA rings mimick prebiotic and early life evolution. METHODS Distances between RNA rings were calculated using different evolutionary models. Associations between these distances and genetic code evolutionary hypotheses detect evolutionary models best describing RNA ring diversification. RESULTS Here pseudo-phylogenetic analyses of RNA rings produce clusters corresponding to the primordial code in tRNA acceptor stems, more so when substitution matrices from neutrally evolving pseudogenes are used rather than from functional protein coding genes reflecting selection for conserving amino acid properties. CONCLUSIONS Results indicate RNA rings with recent cognates evolved from those with early cognates. Hence RNA rings, as designed by the genetic code's structure, simulate tRNA stem evolution and prebiotic history along neutral chemistry-driven mutation regimes.

中文翻译：

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原始的tRNA受体干码来自理论上最小的RNA环簇。

背景技术理论上最小的RNA环通过设计在最短的长度上对20个氨基酸（起始密码子和终止密码子）中的每一个进行一次编码，并形成茎环发夹。这最多定义了22个核苷酸的25个RNA环。作为一个整体，RNA环模仿了许多益生元和生命早期的生物分子特性：tRNA，脱氨梯度和复制起点，天然圆形密码子密码子偏好的出现以及早期蛋白质编码基因的内容。这些特性来自RNA环的计算机电子设计，主要基于重叠翻译框架之间的编码非冗余，这取决于遗传密码的密码子氨基酸分配。RNA环类似于祖先的tRNA，定义了RNA环的反密码子和相应的同源氨基酸。出奇，所有检查过的RNA环特性都与RNA环认知的遗传密码整合等级一起发展，就好像RNA环模仿了益生元和早期生命进化一样。方法使用不同的进化模型计算RNA环之间的距离。这些距离与遗传密码进化假说之间的关联可检测出最能描述RNA环多样化的进化模型。结果在这里，RNA环的假系统发生分析产生了与tRNA受体茎中原始密码相对应的簇，当使用来自中性进化的假基因的替代矩阵而不是来自功能性蛋白质编码基因的替代矩阵时，簇更能反映出氨基酸的保守性，因此更是如此。结论结果表明，具有新近同源的RNA环从早期有同源的RNA环进化而来。因此，RNA环