Parts

Overview

Our parts consist of four single-stranded DNA aptamers which bind to bacteria Escherichia coli ATCC 25922, Salmonella typhimurium, Penicillin G (or Benzylpenicillin), ToX R. The aptamer sequences were obtained from the literature. We created an aptamer collection consisting of four single-stranded DNA aptamers with corresponding part numbers: BBa_K4391000, BBa_K4391001, BBa_K4391002 and BBa_K4391003. Aptamers were ordered from IDT in the form of custom DNA oligos.

We have characterized the aptamers using gradient asymmetric PCR followed by gel electrophoresis to confirm the size. The aptamers have been cloned into the plasmid vector pUC19 and transformed into Escherichia coli DH5α. We have also attached the aptamers for E. coli to GO/PANI (Graphene oxide and Polyaniline) over a glassy carbon electrode and performed cyclic voltammetry and Electrochemical Impedance Spectroscopy (EIS). Then the sensitivity of the aptamer against E. coli and Penicillin G was measured. We have also modelled all three aptamers- generated 2D and 3D folded structures, followed by molecular docking to respective targets.

This part collection can selectively detect E. coli (ATCC 25922), S. Typhimurium, and Penicillin G. Our aptamer collection can be useful for other iGEM teams and scientific communities because each aptamer can play an important role in the development of diagnostics to detect these microbes. Moreover, the molecules our aptamers target are very common and cause several infectious diseases, so the aptamer collection can be beneficial. They comply with all RFC standards of interest to iGEM, so they can also be combined with other biobricks and be delivered together with other constructs.

Parts Table

Name	Type	Description	Designer	Length
BBa_K4391000	Basic Part	E. coli ATCC25922 Aptamer	Prerna Swarnim and Udbhas Garai	78
BBa_K4391001	Basic Part	Penicillin G Aptamer	Prerna Swarnim and Udbhas Garai	98
BBa_K4391002	Basic Part	S. typhimurium Aptamer	Prerna Swarnim and Udbhas Garai	87
BBa_K4391003	Basic Part	Tox R Aptamer	Kalyandeep Ghosh and Udbhas Garai	70

References

1. Marton S et al. (2016) Isolation of an Aptamer that Binds Specifically to E. coli. PLoS ONE 11(4): e0153637. doi:10.1371/ journal.pone.0153637
2. Duan, Nuo & Wu et. al (2013). Selection and Characterization of Aptamers against Salmonella typhimurium Using Whole-Bacterium Systemic Evolution of Ligands by Exponential Enrichment (SELEX). Journal of agricultural and food chemistry. 61. 10.1021/jf400767d.
3. Paniele Nathalie et.al. (2017).Selection of DNA aptamers against penicillin G using Capture-SELEX for the development of an impedimetric sensor. http://dx.doi.org/10.1016/j.talanta.2016.09.058