cRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities

Area of Science:

• Molecular Biology
• Bioinformatics
• RNA Biology

Background:

• Circular RNAs (circRNAs) are a distinct class of non-coding RNA molecules characterized by a covalently closed loop structure.
• circRNAs play significant roles in biological processes, holding potential for clinical and research applications.
• Accurate modeling of circRNA structure and stability is essential for understanding their functions and advancing RNA-based therapeutics.

Purpose of the Study:

• To develop a user-friendly web server, cRNAsp12, for predicting circular RNA secondary structures and folding stabilities.
• To provide a tool that aids in the understanding of circRNA functions and the development of RNA therapeutics.

Main Methods:

• The cRNAsp12 server utilizes a helix-based landscape partitioning strategy to generate distinct structural ensembles.
• It predicts minimal free energy structures within each ensemble using recursive partition function calculations and backtracking algorithms.
• The server allows users to impose structural constraints, such as forcing base pairs or unpaired bases, for refined structure prediction.

Main Results:

• The cRNAsp12 server successfully predicts circular RNA secondary structures and folding stabilities from sequence data.
• It offers a method for generating and analyzing diverse structural ensembles.
• The tool enables constrained predictions, focusing on specific structural features.

Conclusions:

• The cRNAsp12 server provides a valuable resource for researchers studying circular RNA structure and stability.
• This tool can facilitate the investigation of circRNA functions and the design of novel RNA-based therapeutics.
• The user-friendly interface and advanced prediction methods enhance the study of circRNA biology.