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Related Experiment Videos

AOBase: a database for antisense oligonucleotides selection and design.

Xiaochen Bo1, Shaoke Lou, Daochun Sun

  • 1Beijing Institute of Radiation Medicine, Beijing 100850, China.

Nucleic Acids Research
|December 31, 2005
PubMed
Summary

Antisense oligonucleotides (ODNs) are key for gene silencing. The AOBase database collects and shares information on effective and ineffective ODNs, aiding research and rational design for therapeutic applications.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Drug Discovery

Background:

  • Antisense oligonucleotides (ODNs) are crucial for sequence-specific gene expression knockdown.
  • ODNs serve as research tools and therapeutic agents in the post-genome era.
  • Designing effective ODNs requires identifying optimal RNA target sites, a challenging task.

Purpose of the Study:

  • To establish AOBase, a centralized repository for published antisense ODNs.
  • To facilitate the sharing of experimental data on valid and invalid ODNs.
  • To support the development of rational ODN design strategies.

Main Methods:

  • Literature screening to identify and collect data on antisense ODNs.
  • Data curation and storage in the AOBase database.

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  • Development of web-based retrieval interfaces (TargetSearch and AOSearch).

    • Main Results:

    • AOBase contains approximately 700 ODNs targeting 46 different mRNAs.
    • The database includes both validated and invalidated ODNs from published literature.
    • Web interfaces allow for efficient exploration and retrieval of ODN data.

    Conclusions:

    • AOBase serves as a valuable resource for selecting ODNs in gene function studies.
    • The database contributes to rule mining and algorithm development for rational ODN design.
    • AOBase promotes data sharing and advances antisense oligonucleotide technology.