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Parts Overview
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Parts Overview

All our parts were synthesized as gBlocks by IDT with the exception of oprf which was synthesized by Twist Bioscience. Most of the sequences for the genes were obtained from our chassis organism Shewanella oneidensis MR-1 while the others were obtained from Pseudomonas aeruginosa or Escherichia coli MP021561.2 and codon optimized for S. oneidensis MR-1. Our parts were assembled into our backbone pcD8 (Keitz Lab, University of Texas Austin)1 for expression in S. oneidensis MR-1 using the Golden Gate cloning method, where our parts were already synthesized to include the Golden Gate primers. We created an aptamer collection, which consists of five single stranded DNA aptamers, with corresponding part numbers: BBa_K3724001 - BBa_K3724006 (BBa_K3724002 has been deleted). We went through several design-build-test cycles for the asymmetric PCR conditions, in order to optimize the percentage and concentration of ssDNA. We obtained an exceptionally high ssDNA:dsDNA ratio of 7:1 for all optimized aptamers, and concentrations in the 7 - 90 µg/mL range. This part collection can be used to selectively inhibit signaling of three pro-inflammatory cytokines (IL-1β, IL-6, TNF-α), as well as acute immune response protein CRP, and antimicrobial peptide lactoferrin. With detection limits in picomolar range, our aptamer collection can serve as a useful tool for other iGEM teams because each aptamer can be part of potential treatments for various diseases that result in an overactive immune response. Currently it is used in the detection of biomarkers for sepsis diagnosis. Moreover, the molecules our aptamers target are important in cancer, so the aptamer collection can also be part of a cancer detection tool. 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

Favorite Name Type Description Designer Length
BBa_K3724001 Basic IL-6 aptamer Anca Gabriela Frasineanu 57
BBa_K3724003 Basic TNF-α aptamer Anca Gabriela Frasineanu 25
BBa_K3724004 Basic CRP aptamer Anca Gabriela Frasineanu 44
BBa_K3724005 Basic Lactoferrin Aptamer Anca Gabriela Frasineanu 59
BBa_K3724006 Basic IL-1β aptamer Anca Gabriela Frasineanu 30
BBa_K3724008 Coding Diguanylate cyclase YdeH Tracey Moyston 921
BBa_K3724009 Coding Tetraheme cytochrome c protein/ quinol dehydrogenase cymA Tracey Moyston 593
BBa_K3724010 Coding Riboflavin biosynthesis protein RibF Tracey Moyston 966
BBa_K3724011 Coding Outer Membrane Porin OprF Tracey Moyston 1083
BBa_K3724015 Composite Riboflavin synthesis gene cluster Tracey Moyston 3564


  1. ACS Synth. Biol. 2020, 9, 9, 2301–2315Publication Date:July 28, 2020