JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs

Area of Science:

• Structural Biology
• Bioinformatics
• RNA Biology

Background:

• Non-coding RNAs (ncRNAs) play crucial roles and often function via complex 2D and 3D structures.
• While secondary structure diagrams often depict loops as unstructured, 3D analyses reveal they are stabilized by non-canonical base pairs and stacking interactions.
• Diverse RNA sequences can converge to form identical three-dimensional structural motifs.

Purpose of the Study:

• To develop a computational tool, JAR3D, for predicting three-dimensional (3D) structures of RNA hairpin and internal loops.
• To identify potential 3D geometries for RNA loops by comparing their sequences against a curated database of known RNA 3D motifs.
• To provide a webserver for researchers to analyze RNA loop structures and their sequence-structure relationships.

Main Methods:

• JAR3D employs sequence matching, probabilistic scoring, and edit distance algorithms to compare input loop sequences against the RNA 3D Motif Atlas.
• The tool assesses the likelihood of a given sequence adopting the specific interaction patterns characteristic of known 3D motifs.
• A webserver accepts single or multiple loop sequences, or longer RNA sequences containing multiple loops, for analysis.

Main Results:

• JAR3D identifies the top ten most probable RNA 3D Motif Atlas groups for each input sequence.
• The output allows users to align their sequences with the predicted motif groups, facilitating detailed structural interpretation.
• The performance of JAR3D is expected to improve as the RNA 3D Motif Atlas is continuously updated.

Conclusions:

• JAR3D offers a valuable computational approach for predicting and understanding the 3D structures of RNA hairpin and internal loops.
• The tool bridges the gap between sequence information and complex 3D structural motifs in RNA.
• By leveraging the RNA 3D Motif Atlas, JAR3D aids in the discovery and characterization of RNA structural diversity and function.