Pratt Alyssa A, Hendrix David A
Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA.
School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon 97331, USA.
RNA. 2025 Jun 16;31(7):885-895. doi: 10.1261/rna.080176.124.
The sequence of nucleotides that make up an RNA determines its structure, which determines its function. The RNA hairpin, also known as a stem-loop, is a ubiquitous and fundamental feature of RNA secondary structure. A common method of randomizing an RNA sequence is dinucleotide shuffling with the Altschul-Erickson algorithm, which preserves the dinucleotide content of the sequence. This algorithm generates randomized sequences by sampling Eulerian paths through the de Bruijn graph representation of the original sequence. We identified a subset of RNA hairpins in the bpRNA-1m meta-database that always form hairpins after repeated application of dinucleotide shuffling. We investigated these "unbreakable hairpins" and found several common properties. First, we found that unbreakable hairpins had on average similar folding energies compared to other hairpins of similar lengths, although they frequently contained ultra-stable hairpin loops. We found that they tend to be split by purines and pyrimidines on opposite sides of the stem. Furthermore, we found that this specific sequence feature restricts the number of distinct Eulerian paths through their de Bruijn graph representation, resulting in a small number of distinguishable dinucleotide-shuffled sequences. Beyond this algorithmic means of identification, these distinct sequences may have biological significance because we found that a significant percentage occur in a specific location of 16S ribosomal RNAs.
构成RNA的核苷酸序列决定其结构，而结构又决定其功能。RNA发夹结构，也称为茎环结构，是RNA二级结构中普遍存在的基本特征。一种使RNA序列随机化的常用方法是使用阿尔茨舒尔-埃里克森算法进行双核苷酸改组，该算法可保留序列的双核苷酸含量。此算法通过对原始序列的德布鲁因图表示中的欧拉路径进行采样来生成随机序列。我们在bpRNA-1m元数据库中鉴定出了一部分RNA发夹结构，在反复应用双核苷酸改组后它们总是会形成发夹结构。我们对这些“不可破坏的发夹结构”进行了研究，并发现了几个共同特性。首先，我们发现与其他长度相似的发夹结构相比，不可破坏的发夹结构平均具有相似的折叠能，尽管它们经常包含超稳定的发夹环。我们发现它们往往在茎的相对两侧被嘌呤和嘧啶分隔开。此外，我们发现这种特定的序列特征限制了通过其德布鲁因图表示的不同欧拉路径的数量，从而导致可区分的双核苷酸改组序列数量较少。除了这种算法识别方法外，这些独特的序列可能具有生物学意义，因为我们发现相当大比例的序列出现在16S核糖体RNA的特定位置。
