INRS - Institut Armand-Frappier, Laval, QC H7V 1B7, Canada.
Software Engineering and Computer Science Department, Concordia University, Montreal, Quebec H3G 1M8, Canada.
RNA. 2023 Jun;29(6):764-776. doi: 10.1261/rna.079148.122. Epub 2023 Mar 3.
The design of new RNA sequences that retain the function of a model RNA structure is a challenge in bioinformatics because of the structural complexity of these molecules. RNA can fold into its secondary and tertiary structures by forming stem-loops and pseudoknots. A pseudoknot is a set of base pairs between a region within a stem-loop and nucleotides outside of this stem-loop; this motif is very important for numerous functional structures. It is important for any computational design algorithm to take into account these interactions to give a reliable result for any structures that include pseudoknots. In our study, we experimentally validated synthetic ribozymes designed by Enzymer, which implements algorithms allowing for the design of pseudoknots. Enzymer is a program that uses an inverse folding approach to design pseudoknotted RNAs; we used it in this study to design two types of ribozymes. The ribozymes tested were the hammerhead and the , which have a self-cleaving activity that allows them to liberate the new RNA genome copy during rolling-circle replication or to control the expression of the downstream genes, respectively. We demonstrated the efficiency of Enzymer by showing that the pseudoknotted hammerhead and ribozymes sequences it designed were extensively modified compared to wild-type sequences and were still active.
设计保留模型 RNA 结构功能的新 RNA 序列是生物信息学中的一个挑战，因为这些分子的结构非常复杂。RNA 可以通过形成茎环和假结来折叠成二级和三级结构。假结是茎环内的一个区域与该茎环外的核苷酸之间的碱基对集合；这种基序对于许多功能结构非常重要。对于任何包含假结的结构，任何计算设计算法都必须考虑到这些相互作用，以给出可靠的结果。在我们的研究中，我们通过实验验证了 Enzymer 设计的合成核酶，该设计算法允许设计假结。Enzymer 是一个使用反折叠方法设计假结 RNA 的程序；我们在这项研究中使用它来设计两种类型的核酶。所测试的核酶是锤头核酶和发夹核酶，它们具有自我切割活性，使其能够在滚环复制过程中释放新的 RNA 基因组副本，或者分别控制下游基因的表达。我们通过展示 Enzymer 设计的假结锤头核酶和发夹核酶序列与野生型序列相比有广泛的修饰，但仍然具有活性，证明了其效率。
