RNABP COGEST: a resource for investigating functional RNAs

Area of Science:

• Structural bioinformatics
• RNA biology
• Computational chemistry

Background:

• Non-coding RNAs (ncRNAs) are crucial for gene regulation and development, yet their structures and functions remain largely unknown.
• Existing RNA structural databases primarily use 3D structures and base pairing geometry, lacking direct information on stabilization energies.
• Accurate quantification of base pair interaction energies is essential for understanding RNA dynamics and is achievable through Quantum Mechanical (QM) computations.

Purpose of the Study:

• To develop a comprehensive database, 'RNA Base Pair Count, Geometry and Stability' (RNABPCOGEST), consolidating information on non-canonical RNA base pairs.
• To integrate occurrence frequency, experimental and QM-optimized geometries, and computed interaction energies for these base pairs.
• To facilitate the identification of relevant biological model systems for the QM community and provide theoretical insights for the biology community.

Main Methods:

• Literature data mining for non-canonical base pairs in functional RNA structures.
• Extraction of occurrence frequency and base pairing geometry information.
• Computation of interaction energies using Quantum Mechanical (QM) methods.

Main Results:

• Compilation of a non-redundant dataset of functional RNA structures.
• Inclusion of occurrence frequency, experimental and QM-optimized geometries for non-canonical base pairs.
• Provision of computed interaction energies for these base pairs.

Conclusions:

• The RNABPCOGEST database serves as a valuable resource for both QM and biology researchers.
• It enables the selection of appropriate model systems for computational studies.
• It promotes hypothesis-driven biological research by providing theoretical insights into RNA structure and stability.