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Related Experiment Videos

Rational selection of antisense oligonucleotide sequences.

L Smith1, K B Andersen, L Hovgaard

  • 1Department of Pharmaceutics, The Royal Danish School of Pharmacy, Universitetsparken 2, DK-2100, Copenhagen, Denmark.

European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences
|October 24, 2000
PubMed
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This review identifies rational methods for selecting optimal antisense oligonucleotide sequences. It covers finding hybridization sites and binding to structured RNA using computational and empirical techniques.

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Drug Discovery

Background:

  • Antisense oligonucleotides (ASOs) are short nucleic acid sequences designed to modulate gene expression.
  • Identifying effective ASO sequences is crucial for therapeutic applications.
  • RNA secondary structures can impede ASO binding and efficacy.

Purpose of the Study:

  • To review rational selection procedures for optimal antisense oligonucleotide sequences.
  • To identify methods for selecting sequences that effectively bind to target RNA, including structured regions.
  • To provide resources for computational analysis of ASO design.

Main Methods:

  • Review of empirical methods involving large-scale screening of mRNA complementary sequences.
  • Analysis of systematic techniques such as RNase H mapping and combinatorial arrays.

Related Experiment Videos

  • Evaluation of computational methods for predicting RNA secondary structure and ASO binding sites.
  • Discussion of specialized structures like aptastrucs, tethered oligonucleotide probes, and foldback triplex-forming oligonucleotides.

    • Main Results:

    • A range of methods exist for ASO sequence selection, from empirical to computational.
    • Computational approaches offer systematic ways to predict hybridization sites and account for RNA secondary structures.
    • Specialized oligonucleotide structures can be employed to overcome challenges posed by structured RNA targets.
    • Resources and examples for computational ASO design are provided.

    Conclusions:

    • Rational selection procedures are essential for identifying optimal antisense oligonucleotide sequences.
    • A combination of computational and empirical methods, alongside consideration of RNA structure, enhances ASO design.
    • The review provides valuable insights and resources for researchers in the field of antisense technology.