Team:Strasbourg/Aptamers

iGEM

Possible aptazymes for allergen detection

iGEM Strasbourg team is working on the development of a new detection system, which is based on a triple hybrid system (BH3) implemented in E. coli. The flexibility of our system will be provided thanks to an aptazyme which can be interchanged for the detection of a specific ligand. The aptazyme switch is an RNA molecule that has an aptamer domain and a ribozyme domain breakthroughs in molecular biology.
This year we designed this system and tried to optimize experimental conditions by using previously characterized aptazymes. Two different aptazymes were selected: guanosine switch-on (auto-cleavage in presence of ligand) and theophylline switch-off (auto-cleavage in absence of ligand). For future investigation, we propose hypothetical sequences of allergen-specific aptazymes. The aptamers were found in previous publication (cited below) and communication modules, and the ribozyme were described in Felleti et al., 2016 [1].

The SD and the anti-SD sequences are represented in green. The aptamers are in cyan. The communication modules are represented in yellow.

Milk

Detection molecule : Sialyllactose, heterozide, hydrocarbures.

Masud, M, et al. "Sialyllactose-binding modified DNA aptamer bearing additional functionality by SELEX." Bioorganic & Medicinal Chemistry, 12 (2004): 1111-1120

Gluten

Detection molecule : Gli4, peptide.

Gonzalez, S, et. al. "Aptamer Binding to Celiac Disease-Triggering Hydrophobic Proteins A Sensitive Gluten Detection Approach." 2014. Analytical Chemistry 86: 2733-39.

Peanuts

Detection molecule: Arachin, peptide

Tah, A., Olmos Cordero, J.M., Weng, X., and Neethirajan, S. (2018). Aptamer-based biosensor for food allergen determination using graphene oxide/gold nanocomposite on a paper-assisted analytical device (Bioengineering). The potential structure is produced by RNAFold online application http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi.

Eggs

Detection molecule : LC6 and LC15, peptides

Long, Y., Qin, Z., Duan, M., Li, S., Wu, X., Lin, W., Li, J., Zhao, Z., Liu, J., Xiong, D., et al. (2016). Screening and identification of DNA aptamers toward Schistosoma japonicum eggs via SELEX. Sci Rep 6, 24986.

References

  1. Felletti, M., Stifel, J., Wurmthaler, L. A., Geiger, S., Hartig, J. S. 2016. Twister ribozymes as highly versatile expression platforms for artificial riboswitches. Nature Communications.
  2. Masud, M., et al. 2004. Sialyllactose-binding modified DNA aptamer bearing additional functionality by SELEX. Bioorganic & Medicinal Chemistry 12 : 1111-1120.
  3. Gonzalez, S., et. al. 2014. Aptamer Binding to Celiac Disease-Triggering Hydrophobic Proteins A Sensitive Gluten Detection Approach. Analytical Chemistry 86: 2733-39.
  4. Tah, A., Olmos Cordero, J. M., Weng, X., Neethirajan, S. 2018. Aptamer-based biosensor for food allergen determination using graphene oxide/gold nanocomposite on a paper-assisted analytical device (Bioengineering). The potential structure is produced by RNAFold online application http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi.
  5. Long, Y., Qin, Z., Duan, M., Li, S., Wu, X., Lin, W., Li, J., Zhao, Z., Liu, J., Xiong, D., et al. 2016. Screening and identification of DNA aptamers toward Schistosoma japonicum eggs via SELEX. Sci Rep 6, 24986.