Original title: Unraveling Unbreakable Hairpins: Characterizing RNA secondary structures that are persistent after dinucleotide shuffling
Authors: Alyssa A Pratt,David A Hendrix
In this article, the researchers discuss the importance of the sequence of nucleotides in determining the structure and function of RNA. They specifically focus on RNA hairpins, which are a common feature of RNA secondary structure. The researchers used a method called dinucleotide shuffling to randomize the RNA sequence while preserving its dinucleotide content. They discovered a subset of RNA hairpins, called “unbreakable hairpins,” that consistently formed hairpin structures even after repeated shuffling. These unbreakable hairpins had similar folding energies as other hairpins but often contained ultra-stable loops. The researchers also found that these hairpins were split by specific purines and pyrimidines on opposite strands. Furthermore, they observed that these specific hairpins had a limited number of distinguishable shuffled sequences due to the unique features in their sequence. These distinct sequences were also found in a specific location in 16S ribosomal RNAs. Lastly, the researchers developed a formula to calculate the number of possible unique shuffled sequences using the Altschul-Erickson algorithm. Overall, this article highlights the significance of RNA sequence and structure, as well as the potential biological implications of specific hairpin sequences.
Original article: https://www.biorxiv.org/content/10.1101/2023.11.30.569461v1