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The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
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DNAmoreDB, a database of DNAzymes.

Almudena Ponce-Salvatierra1, Pietro Boccaletto1, Janusz M Bujnicki1,2

  • 1Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.

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Summary

DNAzymes are DNA molecules with catalytic abilities, isolated in labs. DNAmoreDB is a new database cataloging these DNA enzymes, their sequences, reactions, and kinetic data for researchers.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Bioinformatics

Background:

  • Deoxyribozymes (DNAzymes) are single-stranded DNA molecules with catalytic functions, analogous to protein enzymes and ribozymes.
  • While not found naturally, DNAzymes are engineered in vitro and can catalyze diverse reactions using various substrates.
  • These engineered DNA enzymes offer potential applications in synthetic biology and chemical synthesis.

Purpose of the Study:

  • To establish DNAmoreDB, a centralized, comprehensive database for deoxyribozymes (DNAzymes).
  • To organize and provide access to critical DNAzyme information, including sequences, selection conditions, catalyzed reactions, kinetics, and literature.
  • To facilitate DNAzyme research by offering search functionalities and a machine-readable API.

Main Methods:

  • In vitro selection was used to isolate DNAzyme sequences with specific catalytic activities.
  • A comprehensive database, DNAmoreDB, was developed to curate and store DNAzyme-related data.
  • Features such as keyword search, BLASTN, a data submission form, and a RESTful API were implemented.

Main Results:

  • DNAmoreDB currently houses information on DNAzymes catalyzing 20 distinct chemical reactions.
  • The database includes sequences, selection parameters, kinetic data, substrates, cofactors, and structural information where available.
  • A user-friendly interface with search capabilities and data retrieval options via API is provided.

Conclusions:

  • DNAmoreDB serves as a valuable, publicly accessible resource for the scientific community studying DNAzymes.
  • The database aims to accelerate DNAzyme discovery and application by consolidating dispersed information.
  • Future updates will expand the database with new DNAzyme data and functionalities.