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Some theoretical aspects of reprogramming the standard genetic code
bioRxiv - Synthetic Biology Pub Date : 2020-09-13 , DOI: 10.1101/2020.09.12.294553
Kuba Nowak , Paweł Błażej , Małgorzata Wnetrzak , Dorota Mackiewicz , Paweł Mackiewicz

Reprogramming of the standard genetic code in order to include non-canonical amino acids (ncAAs) opens a new perspective in medicine, industry and biotechnology. There are several methods of engineering the code, which allow us for storing new genetic information in DNA sequences and transmitting it into the protein world. Here, we investigate the problem of optimal genetic code extension from theoretical perspective. We assume that the new coding system should encode both canonical and new ncAAs using 64 classical codons. What is more, the extended genetic code should be robust to point nucleotide mutation and minimize the possibility of reversion from new to old information. In order to do so, we follow graph theory to study the properties of optimal codon sets, which can encode 20 canonical amino acids and stop coding signal. Finally, we describe the set of vacant codons that could be assigned to new amino acids. Moreover, we discuss the optimal number of the newly incorporated ncAAs and also the optimal size of codon blocks that are assigned to ncAAs.

中文翻译:

重新编程标准遗传密码的一些理论方面

为了包括非规范氨基酸(ncAAs)而对标准遗传密码进行重新编程,为医学,工业和生物技术开辟了新的前景。有多种工程代码的方法,这些方法使我们能够在DNA序列中存储新的遗传信息并将其传递到蛋白质世界中。在这里,我们从理论的角度研究最佳遗传密码扩展的问题。我们假设新的编码系统应使用64个经典密码子对规范和新的ncAA进行编码。此外,扩展的遗传密码应具有较强的鲁棒性,可以指出核苷酸突变,并最大程度地减少了从新信息转换为旧信息的可能性。为此,我们遵循图论研究了最佳密码子集的性质,该密码子集可以编码20个规范氨基酸并停止编码信号。最后,我们描述了可以分配给新氨基酸的空密码子集。此外,我们讨论了新合并的ncAA的最佳数量,以及分配给ncAA的密码子块的最佳大小。
更新日期:2020-09-13
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