Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria.
Methods Mol Biol. 2024;2822:443-469. doi: 10.1007/978-1-0716-3918-4_28.
In vitro selection of allosteric ribozymes has many challenges, such as complex and time-consuming experimental procedures, uncertain results, and the unwanted functionality of the enriched sequences. The precise computational design of allosteric ribozymes is achievable using RNA secondary structure folding principles. The computational design of allosteric ribozymes is based on experimentally validated EAs, random search algorithms, and a partition function for RNA folding. The in silico design achieves an accuracy exceeding 90%. Various algorithms with different logic gates have been automated via computer programs that can quickly create many allosteric sequences. This can eliminate the need for in vitro selection of allosteric ribozymes, thus vastly reducing the time and cost required.
体外筛选变构核酶有许多挑战，如复杂和耗时的实验程序、不确定的结果，以及富集序列的不需要的功能。使用 RNA 二级结构折叠原理可以实现变构核酶的精确计算设计。变构核酶的计算设计基于经过实验验证的 EAs、随机搜索算法和 RNA 折叠的分区函数。计算机模拟设计的准确性超过 90%。通过计算机程序自动实现了各种具有不同逻辑门的算法，这些算法可以快速创建许多变构序列。这可以消除体外筛选变构核酶的需要，从而大大减少所需的时间和成本。
