Part:BBa_K3904705
Aptamer seq 5
Both aptamer lists were generated by our software, firstly EFBALite calculates kinetic energy of initial sequences to create a training dataset for deep learning model later it is employed to speed up computations which helps to iteratively discover new - better aptamers every sequence. Final batches of sequences were generated with 200 genetic algorithm iterations with a help of neural network soft TEA, in silico aptamers have shown high kinetic energy which indicates good affinity with target protein, in this case Albumin; second model that considered aptamers affine to EhPPDK and non-affine to Albumin have been able to identify 10 sequences with low kinetic energy to Albumin also medium-high to EhPPDK.
Introduction
Vilnius-Lithuania iGEM 2021 project AmeByelooks at amebiasis holistically and comprehensively, therefore target E. histolytica from several angles: prevention and diagnostics. Our team's preventive solution consists of probiotics engineered to produce naringenin - an antiprotozoal compound. Two strains of genetically modified microorganisms were chosen as the main chassis - world-renowned Lactobacillus casei BL23 (Lactobacillus paracasei) and Escherichia coli Nissle 1917. Furthermore, the team made specific gene deletions to enhance naringenin production and adapted a novel toxin-antitoxin system to prevent GMO spreads into the environment. The diagnostic part includes a rapid, point of care, user-friendly diagnostic test identifying extraintestinal amebiasis. The main components of this test are aptamers specific to the E. histolytica secreted proteins. These single-stranded DNA sequences fold into tertiary structures for particular fit with target proteins.
Test
This part was not tested for affinity against albumin. Further research is needed.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
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