Team:ETH Zurich/Basic Part

Project

• Description
• Applied Design
• Team Members
• Attributions
• Sponsoring
• Notebook
• Safety
• Downloads

Wet Lab

• Tar Receptor Evolution
• Approach A
• Approach B
• Experiments
• InterLab

Hardware

• Hardware Overview
• Microscope
• Mechanics
• Syringe Pump
• Microfluidic Chip
• Bubbling

Software

• Software Overview
• Motility Readout
• Luminescence Algorithm
• Robot Controls
• Path Planning

Model

• Model Overview
• Integrated Models
• Motility Model
• Split Luciferase Model
• Diffusion Model
• Bubbling Model
• Holographic Imaging Model
• Screening Assay Model
• Model Parameters

Human Practices

• Human Practices
• Education & Engagement

Achievements

• Results
• Parts Overview
• Demonstrate
• Collaborations

Content

Introduction Table

Home

A.R.O.M.A.

Project

• Description
• Applied Design
• Team Members
• Attributions
• Sponsoring
• Notebook
• Safety
• Downloads

Wet Lab

• Tar Receptor Evolution
• Approach A
• Approach B
• Experiments
• InterLab

Hardware

• Hardware Overview
• Microscope
• Mechanics
• Syringe Pump
• Microfluidic Chip
• Bubbling

Software

• Software Overview
• Motility Readout
• Luminescence Algorithm
• Robot Controls
• Path Planning

Model

• Model Overview
• Integrated Models
• Motility Model
• Split Luciferase Model
• Diffusion Model
• Bubbling Model
• Screening Assay Model
• Holographic Imaging Model

Human Practices

• Human Practices
• Education & Engagement

Achievements

• Results
• Parts Overview
• Demonstrate
• Collaborations

Parts.

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No iGEM project without the creation of new biobricks! In total, we submitted 29 parts to the biobrick registry. Click on them to learn more about the individual parts. You can also find a direct link to their respective site in the iGEM parts registry.

Parts

Sticky flagellin protein

BBa_K2845000 - Sticky fliC

Encoding the truncated version of the flagellar protein FliC (BBa_K777109). It still yields a fully functional flagellum, but the individual FliC proteins stick to different surfaces like glass or polystyrene.

BBa_K2845000

Obtained with overhang primers via PCR from FliC (BBa_K777109) from distribution kit.

BBa_K2845001 - Sticky fliC with promoter and RBS

The sticky flic (BBa_K2845000) under a strong Anderson promoter (BBa_J23104) and a weak RBS (BBa_B0032).

BBa_K2845001

Obtained with overhang primers via PCR from FliC (BBa_K777109) from distribution kit.

Building Blocks for the split protein complementation approach

BBa_K2845002 - CLuc

Coding region for the C-terminus of split EPIC Luciferase.

BBa_K2845002

Obtained with overhang primers via PCR from distribution kit template (EPIC Luciferase, BBa_K32510).

BBa_K2845003 - NLuc

Coding region for the N-terminus of split EPIC Luciferase .

BBa_K2845003

Obtained with overhang primers via PCR from distribution kit template (EPIC Luciferase, BBa_K32510).

BBa_K2845004 - CLuc with promoter and RBS

C-terminus of split EPIC Luciferase under the control of a strong Anderson promoter and a medium RBS.

BBa_K2845004

Obtained with overhang primers via PCR from distribution kit template (EPIC Luciferase, BBa_K32510).

BBa_K2845005 - NLuc with promoter and RBS

N-terminus of split EPIC Luciferase under the control of a strong Anderson promoter and a medium RBS.

BBa_K2845005

Obtained with overhang primers via PCR from distribution kit template (EPIC Luciferase, BBa_K32510).

BBa_K2845006 - CLuc-NLuc

Coding region for the C-terminus and the N-terminus of split EPIC Luciferase on a polycistronic mRNA.

BBa_K2845006

Obtained with overhang primers via PCR from distribution kit template (EPIC Luciferase, BBa_K32510), united via GIBSON assembly.

BBa_K2845007 - pOmpC:EPIC_Luc

EPIC luciferase under the control of pOmpC and a medium RBS.

BBa_K2845007

Obtained with overhang primers via PCR from distribution kit template (EPIC Luciferase, BBa_K32510).

BBa_K2845008 - OmpR

Coding region for the OmpR transcription factor

BBa_K2845008

Obtained with overhang primers via PCR from genome of E. coli DH5a.

BBa_K2845009 - OmpR with promoter and RBS

OmpR transcription factor from E. coli’s OmpR/EnvZ two component system involved in osmoregulation under the control of a medium Anderson promoter and a medium RBS.

BBa_K2845009

Obtained with overhang primers via PCR from genome of E. coli DH5a.

Binding site arrangements of ompC and tetO for the split protein complementation approach

BBa_K2845017 - OmpR binding site next to TetR binding site separated by 10 bases.

Assembly of the OmpR binding site ompC and the TetR binding site tetO. Designed to use DNA as a scaffold for transcription factor binding visualization via slit protein complementation.

BBa_K2845017

Binding sites inserted via overhang primers into the operon of pSB1A3 and religated via GIBSON assembly.

BBa_K2845019 - OmpR binding site next to TetR binding site separated by 15 bases.

Assembly of the OmpR binding site ompC and the TetR binding site tetO. Designed to use DNA as a scaffold for transcription factor binding visualization via slit protein complementation.

BBa_K2845019

Binding sites inserted via overhang primers into the operon of pSB1A3 and religated via GIBSON assembly.

BBa_K2845021 - OmpR binding site next to TetR binding site separated by 20 bases.

Assembly of the OmpR binding site ompC and the TetR binding site tetO. Designed to use DNA as a scaffold for transcription factor binding visualization via slit protein complementation.

BBa_K2845021

Binding sites inserted via overhang primers into the operon of pSB1A3 and religated via GIBSON assembly.

BBa_K2845023 - OmpR binding site next to TetR binding site separated by 25 bases.

Assembly of the OmpR binding site ompC and the TetR binding site tetO. Designed to use DNA as a scaffold for transcription factor binding visualization via slit protein complementation.

BBa_K2845023

Binding sites inserted via overhang primers into the operon of pSB1A3 and religated via GIBSON assembly.

BBa_K2845025 - TetR binding site next to OmpR binding site separated by 10 bases.

Assembly of the OmpR binding site ompC and the TetR binding site tetO. Designed to use DNA as a scaffold for transcription factor binding visualization via slit protein complementation.

BBa_K2845025

Binding sites inserted via overhang primers into the operon of pSB1A3 and religated via GIBSON assembly.

BBa_K2845027 - TetR binding site next to OmpR binding site separated by 15 bases.

Assembly of the OmpR binding site ompC and the TetR binding site tetO. Designed to use DNA as a scaffold for transcription factor binding visualization via slit protein complementation.

BBa_K2845027

Binding sites inserted via overhang primers into the operon of pSB1A3 and religated via GIBSON assembly.

BBa_K2845029 - TetR binding site next to OmpR binding site separated by 20 bases.

Assembly of the OmpR binding site ompC and the TetR binding site tetO. Designed to use DNA as a scaffold for transcription factor binding visualization via slit protein complementation.

BBa_K2845029

Binding sites inserted via overhang primers into the operon of pSB1A3 and religated via GIBSON assembly.

BBa_K2845031 - TetR binding site next to OmpR binding site separated by 25 bases.

Assembly of the OmpR binding site ompC and the TetR binding site tetO. Designed to use DNA as a scaffold for transcription factor binding visualization via slit protein complementation.

BBa_K2845031

Binding sites inserted via overhang primers into the operon of pSB1A3 and religated via GIBSON assembly.

Fusion proteins of OmpR and NLuc with different amino acid linkers

BBa_K2845032 - OmpR-FFF-NLuc

Fusion protein consisting of the N-terminus of split EPIC luciferase fused via a flexible linker to OmpR under the control of a medium Anderson promoter (BBa_J23118) and a weak RBS (BBa_B0032).

BBa_K2845032

Obtained with overhang primers via PCR of OmpR and NLuc and religated via GIBSON assembly.

BBa_K2845035 - OmpR-FFF-NLuc, no promoter and RBS

Coding region for a fusion protein consisting of the N-terminus of split EPIC luciferase fused via a flexible linker to OmpR.

BBa_K2845035

Obtained with overhang primers via PCR of OmpR and NLuc and religated via GIBSON assembly.

BBa_K2845037 - OmpR-RFR-NLuc

Fusion protein consisting of the N-terminus of split EPIC luciferase fused via a mixed linker to OmpR under the control of a medium Anderson promoter (BBa_J23118) and a weak RBS (BBa_B0032).

BBa_K2845037

Obtained with overhang primers via PCR of OmpR and NLuc and religated via GIBSON assembly.

BBa_K2845038 - OmpR-RFFF-NLuc

Fusion protein consisting of the N-terminus of split EPIC luciferase fused via a mixed linker to OmpR under the control of a medium Anderson promoter (BBa_J23118) and a weak RBS (BBa_B0032).

BBa_K2845038

Obtained with overhang primers via PCR of OmpR and NLuc and religated via GIBSON assembly.

BBa_K2845041 - OmpR-RFFR-NLuc

Fusion protein consisting of the N-terminus of split EPIC luciferase fused via a mixed linker to OmpR under the control of a medium Anderson promoter (BBa_J23118) and a weak RBS (BBa_B0032).

BBa_K2845041

Obtained with overhang primers via PCR of OmpR and NLuc and religated via GIBSON assembly.

BBa_K2845042 - OmpR-FFFR-NLuc

Fusion protein consisting of the N-terminus of split EPIC luciferase fused via a mixed linker to OmpR under the control of a medium Anderson promoter (BBa_J23118) and a weak RBS (BBa_B0032).

BBa_K2845042

Obtained with overhang primers via PCR of OmpR and NLuc and religated via GIBSON assembly.

BBa_K2845044 - OmpR-FFFR-NLuc

Fusion protein consisting of the N-terminus of split EPIC luciferase fused via a mixed linker to OmpR under the control of a medium Anderson promoter (BBa_J23118) and a weak RBS (BBa_B0032).

BBa_K2845044

Obtained with overhang primers via PCR of OmpR and NLuc and religated via GIBSON assembly.

Fusion proteins of CLuc and TetR with different amino acid linkers

BBa_K2845046 - CLuc-FFF-TetR

Fusion protein consisting of the C-terminus of split EPIC luciferase fused via a flexible linker to TetR under the control of a medium Anderson promoter (BBa_J23118) and a weak RBS (BBa_B0032).

BBa_K2845046

Obtained with overhang primers via PCR of CLuc and TetR and religated via GIBSON assembly.

BBa_K2845047 - CLuc-FRF-TetR

Fusion protein consisting of the C-terminus of split EPIC luciferase fused via a mixed linker to TetR under the control of a medium Anderson promoter (BBa_J23118) and a weak RBS (BBa_B0032).

BBa_K2845047

Obtained with overhang primers via PCR of CLuc and TetR and religated via GIBSON assembly.

BBa_K2845048 - CLuc-RFFR-TetR

Fusion protein consisting of the C-terminus of split EPIC luciferase fused via a mixed linker to TetR under the control of a medium Anderson promoter (BBa_J23118) and a weak RBS (BBa_B0032).

BBa_K2845047

Obtained with overhang primers via PCR of CLuc and TetR and religated via GIBSON assembly.

Tar-EnvZ

BBa_K2845072 - LacI: Tar-EnvZ

Membrane receptor protein allowing the activation of OmpR with aspartate.

BBa_K2845047

Tar-EnvZ ordered as gblock from IDT. Promoter obtained with overhang primers via PCR.

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