BioBrick: Aggregate Parts

1
BioBrick Aggregate Parts
Coding Region
RBS
Promoter
RBS
Terminator
Reporter Coding Region
Terminator
Reporter
Quad Part Inverter (QPI)
2
QPIs and Reporters
Have
Need
LacI QPI
LacI(ts) QPI
Lambda cI QPI
Lambda cI857 QPI
434 cI QPI
mCherry
GFP (mut3b)
Venus
3
Test Constructs
GFP (mut3b)
Plambda
Plambda
Lambda cI QPI
LacI QPI
LacI QPI
GFP (mut3b)
GFP (mut3b)
PLac
Lambda cI QPI
GFP (mut3b)
Plambda
Plambda
Lambda cI QPI
434 QPI
GFP (mut3b)
LacI(ts) QPI
GFP (mut3b)
Plambda
LacI(ts) QPI
GFP (mut3b)
P434
P434
434 QPI
857 QPI
GFP (mut3b)
857 QPI
4
BioBricks Testing
Condition Temp ( C) 30 30 30 30 40 40 40 40
Condition IPTG (-) (-) () () (-) (-) () ()
Condition UV (-) () (-) () (-) () (-) ()
QPIs LacI (-) (-) () () (-) (-) () ()
QPIs lambda (-) () (-) () (-) () (-) ()
QPIs 434 (-) () (-) () (-) () (-) ()
QPIs 857 (-) (-) (-) (-) () () () ()
QPIs LacI(ts) (-) (-) () () () () () ()
Condition Stimulus UV UV heat heat IPTG IPTG none none
Condition Initial State (-) () (-) () (-) () (-) ()
Toggle Switches LacI (Collins) () () (-) () (-) (-) (-) ()
Toggle Switches 857 () () (-) (-) (-) () (-) ()
Toggle Switches LacI(ts) () () (-) (-) (-) (-) (-) ()
5
Things We Want to Know

• Minimal exposure time to UV to switch state
• Minimal concentration of IPTG to switch state
• Minimal exposure time to heat to switch state
• Amount of time a given state is maintained
• Time delay between input and reporting
• Effect of varying cell densities
• Effect of competing inputs
• Does SOS work in stationary phase
• Effectiveness of UV laser pointer

6
Schedule - Week 1
Week 1 Mutation Begin introducing ts mutation into LacI coding region and LacI QPI
Week 1 BioBrick Assembly RBS 857 T Plambda mCherry T Venus T Plambda QPILacI QPIlambda GFP QPI434 GFP
Week 1 Collins
7
Schedule - Week 2
Week 2 Mutation Continue mutations
Week 2 BioBrick Assembly RBS-857 T-Plambda (QPI857) Plambda-QPILac QPIlambda-GFP Plambda-QPILac GFP Plac QPIlambda-GFP Plambda QPI434-GFP RBS mCherry-T RBS Venus-T
Week 2 Collins
8
Schedule - Week 3
Week 3 Mutation Sequence mutations
Week 3 BioBrick Testing Plambda-QPILac-GFP Plac-QPIlambda-GFP Plambda-QPI434-GFP Plambda-QPILac-QPIlambda-GFP (Collins)
Week 3 BioBrick Assembly P434 QPI857
Week 3 Collins
9
Schedule - Week 4
Week 4 BioBrick Testing II Plambda-QPILac-GFP Plac-QPIlambda-GFP Plambda-QPI434-GFP Plambda-QPILac-QPIlambda-GFP (Collins)
Week 4 BioBrick Assembly P434-QPI857 GFP P434-QPI857 QPI434-GFP Plambda QPILac(ts)
Week 4 Collins
10
Schedule - Week 5
Week 5 BioBrick Testing P434-QPI857-GFP P434-QPI857-QPI434-GFP (857 system)
Week 5 BioBrick Assembly Plambda-QPILac(ts) GFP Plambda-QPILac(ts) QPIlambda-GFP
Week 5 Collins
11
Schedule - Week 6
Week 6 BioBrick Testing II P434-QPI857-GFP P434-QPI857-QPI434-GFP (857 system)
Week 6 BioBrick Testing Plambda-QPILac(ts)-GFP Plambda-QPILac(ts)-QPIlambda-GFP (Lac(ts) system)
Week 6 Collins
12
Schedule - Week 7

• Padding