Analysis of the evolution of the thrombin-inhibiting DNA aptamers using a genetic algorithm

Abstract

We previously identified a thrombin-inhibiting DNA aptamer that was presumed to form a G-quartet structure with a duplex. To investigate the importance of the sequences in the duplex region and to obtain aptamers with higher inhibitory activities, we randomized the sequences of the duplex region of this aptamer and carried out selection based on inhibitory activity using a genetic algorithm. This method consisted of selection via an inhibition assay, crossover, and mutation in silico. After two cycles, we obtained ligands with greater inhibitory activities than that of the original aptamer. In addition, the duplex sequences were found to contribute to the inhibitory activities of aptamers.

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Acknowledgment

This work is partly supported by the Grant-in-Aid for the 21st Century COE “Future Nano-Materials” from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan.

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Correspondence to Kazunori Ikebukuro.

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Ikebukuro, K., Yoshida, W., Noma, T. et al. Analysis of the evolution of the thrombin-inhibiting DNA aptamers using a genetic algorithm. Biotechnol Lett 28, 1933–1937 (2006). https://doi.org/10.1007/s10529-006-9174-8

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Keywords

  • Aptamer
  • Genetic algorithm
  • G-quartet structure
  • Inhibitor
  • Systematic evolution of ligands by exponential enrichment