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Related Experiment Videos

Novel strategy for DNA aptamers inhibiting enzymatic activity using algorithm mimicking evolution.

Kazunori Ikebukuro1, Yuji Okumura, Koichi Sumikura

  • 1Department of Biotechnology and Life Science, Tokyo University of Agriculture & Technology, 2-24-16 Naka-machi, Koganei, Tokyo 184-8588, Japan.

Nucleic Acids Research. Supplement (2001)
|September 27, 2003
PubMed
Summary

Researchers developed an evolution-inspired algorithm to screen DNA aptamers that inhibit thrombin. This novel method successfully identified potent thrombin inhibitors, optimizing aptamer sequences for enhanced activity.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Bioinformatics

Background:

  • Thrombin is a key enzyme in blood coagulation.
  • DNA aptamers are promising therapeutic agents due to their specificity and stability.
  • Developing efficient screening methods for high-affinity aptamers is crucial.

Purpose of the Study:

  • To develop and validate a novel, evolution-mimicking algorithm for screening DNA aptamers against thrombin.
  • To identify DNA aptamers with high inhibitory activity against thrombin.
  • To further optimize aptamer sequences for enhanced thrombin inhibition.

Main Methods:

  • Random synthesis of 15-mer oligonucleotides designed to form G-quartet structures.
  • In vitro screening of oligonucleotide inhibitory activity against thrombin.

Related Experiment Videos

  • In silico shuffling and mutation of high-activity aptamers over multiple cycles (5 cycles).
  • In silico modification by adding 8-mer oligonucleotides to the 5' and 3' ends of selected aptamers, followed by 2 additional cycles of evolution.

    • Main Results:

    • The evolution-mimicking algorithm successfully identified DNA aptamers with high thrombin inhibitory activity, including previously reported sequences.
    • Optimization by adding flanking sequences resulted in a new aptamer with superior inhibitory activity compared to the original 15-mer aptamer.

    Conclusions:

    • An evolution-mimicking computational approach is effective for screening and optimizing DNA aptamers.
    • The developed method can identify potent aptamers and enhance their inhibitory efficacy through sequence modification.
    • This strategy offers a powerful tool for aptamer discovery and development in therapeutic applications.