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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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StructRMDB: A database of RNA modification sites that affect RNA secondary structure.

Ziyan Zhang1,2, Xuan Wang1,3, Jingxian Zhou4,5,6

  • 1Department of Biosciences and Bioinformatics, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.

Computational and Structural Biotechnology Journal
|December 24, 2025
PubMed
Summary

StructRMDB is the first database detailing how chemical modifications like N6-Methyladenosine (m6A) alter RNA secondary structures. It provides insights into RNA structure changes impacting biological processes.

Keywords:
Adenosine-to-inosine editingN6-methyladenosinePseudouridineRNA modificationRNA secondary structure

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Post-transcriptional RNA modifications are crucial for biological processes, affecting RNA structure and function.
  • Advancements in prediction algorithms enable RNA secondary structure prediction for modified RNA sequences.

Purpose of the Study:

  • Introduce StructRMDB, the first database to characterize the impact of chemical modifications on RNA secondary structure.
  • Provide a comprehensive resource for studying RNA modification effects on structure.

Main Methods:

  • Compiled over 880,000 RNA modification sites and their structural impacts from nine species.
  • Utilized RNAstructure and ViennaRNA tools with four scoring methods to assess structural changes.
  • Visualized RNA secondary structures with and without modifications to highlight alterations.

Main Results:

  • StructRMDB includes data on N6-Methyladenosine (m6A), pseudouridine (Ψ), and adenosine-to-inosine editing (A-to-I) in pre- and mature RNA.
  • Quantified structural impacts using Similarity Score, Relative Score, Distance, and SMC Score.
  • Demonstrated significant structural alterations induced by RNA modifications.

Conclusions:

  • StructRMDB offers novel insights into the effects of RNA modifications on secondary structure.
  • Serves as a valuable resource for researchers studying RNA structure and function.
  • Provides a user-friendly interface for accessing, downloading, and sharing modification data.