• Introduction
  • Home
  • The Team
  • Photo Gallery
• Our Project
  • Results Summary
  • Selection System
  • In-Vitro Characterization
  • In-Vivo Characterization
  • Microfluidics
  • Data
  • Attributions
• Tools
  • Gibson Assembly
  • MITOMI
• Notebook
  • Protocols
  • May
  • June
  • July
  • August
  • September
  • October
• Considerations
  • Human Practices
  • Safety
• Acknowledgements
  • Sponsors
  • Partners

Data

team, please check this page: [1]

Overview

Summary

There are three pillars that underlie our transcription factor development pipeline. The first pillar is a selection system which lyses cells containing strong matches between a transcription factor and its promoter and allows for the speedy recovery of the relevant DNA. The second pillar is an in vivo characterization system that uses two different reporter systems as a way to document the binding affinities of the TetR transcription factor and its promoter pTet. The third pillar is an in-vitro characterization system called MITOMI that allows for high-throughput analysis of DNA-protein interaction strengths.

In developing these three pillars, a number of parts were made. We have listed all of them and have highlighted our favorites.

Systems

Selection System: We cloned the Berkeley Lysis cassette (BBa_K112808) under control of the T7 promoter into a low copy number plasmid (pSB3K1, formerly BBa_I739202).

In Vivo Characterization:

In Vitro Characterization:

Biobricks

Favourite parts

[http://partsregistry.org/Part:BBa_K613015 BBa_K613015]

[http://partsregistry.org/Part:BBa_K613016 BBa_K613016]

[http://partsregistry.org/Part:BBa_K613017 BBa_K613017]

Pre-existing parts characterised

• [http://partsregistry.org/Part:BBa_K112808:Experience Experience] - The Berkeley Lysis Device, BBa_K112808: In developing our Lysis selection device, we characterised induction, and ran proof-of-principle experiments.

All other parts submitted

TetR Mutants

• V36F mutant: [http://partsregistry.org/Part:BBa_K613013 K613013]
• V36F W43S double mutant: [http://partsregistry.org/Part:BBa_K613014 K613014]
• E37A W43S T141A triple mutant: [http://partsregistry.org/Part:BBa_K613015 K613015]
• P39K mutant: [http://partsregistry.org/Part:BBa_K613016 K613016]
• Y42F K108E double mutant: [http://partsregistry.org/Part:BBa_K613018 K613018]
• P39Q Y42M double mutant: [http://partsregistry.org/Part:BBa_K613019 K613019]

T7 Promoter variants

Our lysis selection device uses what we refer to as the wild-type T7 Promoter:

[http://partsregistry.org/Part:BBa_K613001 K613001]

In addition, we submitted the following mutants:

Variants without additional lac operator (constitutive):

[http://partsregistry.org/Part:BBa_K613002 K613002]

[http://partsregistry.org/Part:BBa_K613003 K613003]

[http://partsregistry.org/Part:BBa_K613004 K613004]

[http://partsregistry.org/Part:BBa_K613005 K613005]

[http://partsregistry.org/Part:BBa_K613006 K613006]

Variants with additional lac operator (LacI repressed):

[http://partsregistry.org/Part:BBa_K613007 K613007]

[http://partsregistry.org/Part:BBa_K613008 K613008]

[http://partsregistry.org/Part:BBa_K613009 K613009]

[http://partsregistry.org/Part:BBa_K613010 K613010]

[http://partsregistry.org/Part:BBa_K613011 K613011]

[http://partsregistry.org/Part:BBa_K613012 K613012]

Medium-strength Plac

[http://partsregistry.org/Part:BBa_K613000 K613000]