- Wet Lab
- Dry Lab
- Human Practices
Our project involved the creation of a range of genetic parts, which served a plethora of purposes, most importantly, the creation and evaluation of our MEDEA genetic system, as well as the validation of their activity. Some parts were designed and measured using software: aptamers were created using MPDR and modified hammerhead ribozymes were synthesized after their structure had been predicted using RNADock, RNA Composer and Chimera visualized (for more information, see Software and Modelling respectively).
We designed most of our parts so that they are both 3A Assembly and Golden Gate compatible. In this way, our parts were assembled into iGEM plasmid such as pSB1C3, in order to be validated, and the complete CIRCE plasmid was constructed via a Golden Gate assembly reaction, see Protocols. This way, we could use the same sequences for both purposes, a feature which could have great use in improving Access to Synthetic Biology.
During the development of our project, we managed to synthesize the following parts.
Name Type Short Description Designer Length BBa_K3201000 Coding nCpf1 (RNA-guided DNA nickase) Anastasios Galanis 3921 BBa_K3201001 RNA Small transcription activating RNA (STAR) Anastasios Galanis 61 BBa_K3201002 RNA S.mansoni Type 1 Hammerhead Ribozyme Anastasios Galanis, Nikolaos Karvelas 63 BBa_K3201003 RNA S.mansoni Type 1 Hammerhead Ribozyme with STAR module Nikolaos Karvelas, Anastasios Galanis 132 BBa_K3201004 RNA S.mansoni Type 1 Hammerhead Ribozyme, Inactive Nikolaos Karvelas 63 BBa_K3201005 RNA S.mansoni Type 1 Hammerhead Ribozyme, Cpf1 Optimised Nikolaos Karvelas, Anastasios Galanis 64 BBa_K3201006 Regulatory Small Transcription Activating RNA Target Sequence (STAR Target) Nikolaos Karvelas 100 BBa_K3201007 Coding Fidelity-reduced DNA Polymerase PolI3M Nikolaos Karvelas 2987 BBa_K3201008 Composite nCpf1 (Cas12) - PolI3M fusion Nikolaos Karvelas, Anastasios Galanis 6938 BBa_K3201009 Regulatory araC-Pbad and STAR target sequence Nikolaos Karvelas 1317 BBa_K3201010 Coding Antibiotic Cassette with aadA and KanR Anastasios Galanis, Nikolaos Kalavros, Nikolaos Karvelas 1789 BBa_K3201011 Composite C-reactive protein Nikolaos Karvelas, Jason Papadopoulos, Anna-Maria Tsiatsiani 907 BBa_K3201014 Terminator Terminator containg SexAI site Anastasios Galanis 46 BBa_K3201015 Composite Aptamer Basic Cassette (EvolvR) Anastasios Galanis, Nikolaos Karvelas 178 BBa_K3201016 Composite Aptamer Basic Cassette (CIDER) Anastasios Galanis, Nikolaos Karvelas 171 BBa_K3201017 Intermediate gRNA for use with EvolvR system Anastasios Galanis, Nikolaos Karvelas 96 BBa_K3201018 Intermediate gRNA for use with EvolvR system Anastasios Galanis, Nikolaos Karvelas 96 BBa_K3201019 Intermediate crRNA for CIDER Anastasios Galanis, Nikolaos Karvelas 39 BBa_K3201020 Composite pBAD-araC STAR target with aadA and KanR Anastasios Galanis, Nikolaos Karvelas, Nikolaos Kalavros 3106 BBa_K3201021 Plasmid pEKATI (Plasmid for Aptamer Directed Evolution using EvolvR) Anastasios Galanis, Nikolaos Karvelas, Nikolas Kalavros, Fani Zoumpou, Iason Papadopoulos, Anna Maria Tsiatsiani, Alexandra Karvela 15291 BBa_K3201022 Plasmid pCIRCE (Plasmid for Aptamer Directed Evolution using CIDER) Nikolaos Karvelas 15105 BBa_K3201023 Composite STAR target RFP Nikolaos Karvelas 982 BBA_K321024 Plasmid pCHEATE Theofano Zoumpou, Anastasios Galanis, Nikolaos Karvelas, Nikolaos Kalavros 6399