Ribocentre-aptamer: an integrative, structure-focused database for RNA aptamers.

Area of Science:

• Biochemistry
• Molecular Biology
• Bioinformatics

Background:

• RNA aptamers act as chemical antibodies, offering versatile ligand binding for applications in diagnostics, therapeutics, and biosensing.
• Rational aptamer design is currently limited by a lack of integrated resources that connect experimental structural data with ligand-binding mechanisms.

Purpose of the Study:

• To present Ribocentre-aptamer, a manually curated database designed to capture the molecular mechanisms of RNA aptamer binding.
• To provide a comprehensive resource for researchers to advance aptamer science and engineering.

Main Methods:

• Systematic cataloging of 191 aptamer types from 669 publications.
• Integration of 510 RNA sequences, 123 small-molecule ligands, and 344 protein ligands.
• Inclusion of experimentally resolved secondary/tertiary structures, ligand-binding pockets, affinity metrics, and functional annotations.

Main Results:

• The Ribocentre-aptamer database now houses extensive data on RNA aptamer structures and their interactions with various ligands.
• The resource unifies diverse data points, including sequences, ligand types, structural information, and binding affinities.
• Detailed annotations provide insights into the functional aspects of aptamer-ligand binding.

Conclusions:

• Ribocentre-aptamer serves as an indispensable platform for bridging molecular mechanism discovery with translational aptamer engineering.
• The database facilitates a deeper understanding of RNA aptamer behavior, paving the way for improved diagnostic and therapeutic applications.