Analysis of the evolution of the thrombin-inhibiting DNA aptamers using a genetic algorithm
- 240 Downloads
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.
KeywordsAptamer Genetic algorithm G-quartet structure Inhibitor Systematic evolution of ligands by exponential enrichment
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.
- Noma T, Ikebukuro K (2006) Aptamer selection based on inhibitory activity using an evolution-mimicking algorithm. Biochem Biophys Res Commun (in press). DOI 10.1016/j.bbrc.2006.06.083Google Scholar
- Ruckman J, Green LS, Beeson J, Waugh S, Gillette WL, Henninger DD, Claesson-Welsh L, Janjic N (1998) 2-Fluoropyrimidine RNA-based aptamers to the 165-amino acid form of vascular endothelial growth factor (VEGF165). Inhibition of receptor binding and VEGF-induced vascular permeability through interactions requiring the exon 7-encoded domain. J Biol Chem 273:20556–20567PubMedCrossRefGoogle Scholar
- Weber L, Wallbaum S, Broger C, Gubernator K (1995) A genetic algorithm optimizing the biological activity of combinatorial compound libraries. Angew Chem Int Ed Engl 107:2453–2454Google Scholar