Ribocentre-aptamer: an integrative, structure-focused database for RNA aptamers
RNA aptamers function as 'chemical antibodies' with advantages in binding to diverse ligands, enabling transformative applications in diagnostics, therapeutics, and biosensing. Despite these potential and existing databases, rational aptamer design is hindered by the lack of integrated resources coupling experimentally determined structural data with ligand-binding mechanisms. Here, we present Ribocentre-aptamer (https://aptamer.ribocentre.org/), a manually curated database to capture the molecular mechanism of RNA aptamer binding. Our resource systematically catalogues 191 aptamer types across 669 publications, unifying 510 sequences, 123 small-molecule ligands, and 344 protein ligands with experimentally resolved secondary/tertiary structures, ligand-binding pockets, affinity metrics, and functional annotations. Ribocentre-aptamer aims to bridge molecular mechanism discovery with translational engineering, providing an indispensable platform for advancing aptamer science.
Authors
- Bo Fu (ORCID: https://orcid.org/0000-0002-7885-2874)
- Baicheng Huang (ORCID: https://orcid.org/0000-0002-2014-5739)
- Linfei Li (ORCID: https://orcid.org/0000-0002-5217-3005)
- X H Chen (ORCID: https://orcid.org/0000-0002-4502-0633)
- Zhizhong Lu (ORCID: https://orcid.org/0000-0003-1461-9093)
- Zhi-Jie Tan (ORCID: https://orcid.org/0000-0002-7367-0182)
- Qiaozhen Liu
- Zhichao Miao (ORCID: https://orcid.org/0000-0002-5777-9815)
- Lin Huang (ORCID: https://orcid.org/0000-0002-2121-365X)
- Xuemei Peng (ORCID: https://orcid.org/0000-0002-5363-3085)
- Ao Ying (ORCID: https://orcid.org/0009-0004-4091-6088)
- Yingying Zhao (ORCID: https://orcid.org/0000-0002-6170-6125)
- Jiali Wang (ORCID: https://orcid.org/0000-0002-0780-5624)
- Hao Sun (ORCID: https://orcid.org/0000-0001-8829-0468)
- Yuhang Luo
- Yuxuan Sun
- Jiaxin Zhao (ORCID: https://orcid.org/0009-0007-6095-3590)
- Shuang Zhu
- Mengxiao Li (ORCID: https://orcid.org/0000-0003-3949-3503)
- Yan He (ORCID: https://orcid.org/0009-0001-6301-881X)
- Ke Chen (ORCID: https://orcid.org/0009-0005-5702-9597)
- Yuan Ren
- Z. R. Qiu
- Yixin Chen (ORCID: https://orcid.org/0000-0002-4965-8976)
- Ziyu Guo (ORCID: https://orcid.org/0000-0001-9606-9691)
Institutions
- Tongji University (CN)
- Sun Yat-sen University (CN)
- Shenzhen University (CN)
- Guangdong Pharmaceutical University (CN)
- Guangzhou Experimental Station (CN)
- Sun Yat-sen Memorial Hospital (CN)
- Guangdong-Hongkong-Macau Joint Laboratory of Collaborative Innovation for Environmental Quality (CN)
- Shanghai Center for Brain Science and Brain-Inspired Technology (CN)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2025-09-22
- DOI
- https://doi.org/10.1093/nar/gkaf1016
- Citations
- 2
- Primary Topic
- RNA and protein synthesis mechanisms
- Type
- article
- Field-Weighted Citation Impact
- 1.61
Funders
- National Natural Science Foundation of China
- Guangdong Pharmaceutical University