muri pattern detection circuits andrew yang, jonathan babb, ron weiss 9/23/2011

MURI Pattern Detection Circuits

Andrew Yang, Jonathan Babb, Ron Weiss9/23/2011

Null versus 1 Systems (Circuits #1-6)

NOTE: Not depicted is a stretch of DNA following the promoters and preceding the genes called the ‘RBS’. The RBS is tunable, thus controlling the strength of gene expression. Please account for this possibility.

Null Null “1”

Circuit operation: Initial state of toggle set for CI production with IPTG. Later, UV induces state change for a region by cleaving CI. If the region is large enough to achieve an engineering quorum, the quorum is amplified to the entire region and reported by a blue fluorescent protein.

Goal: Digital behavior. Circle sizes willbe smaller or larger than aforbidden band.

UV Toggle 3OC12HSL Quorum Sensor 3OC12HSL Propagator State “1” = 30C12HSL

CI pLasORI LasI LasR mCherryLacI pLacpCI

UV 30C12HSLIPTG

pLas LasI LasR GFP

30C12HSL

Quorum Sensor PropagatorToggle Switch

Quorum sensor activated only in UV exposed region.

Las SystemCircuit #1

Circuit #2: External atc->LasR

atc


UV 30C12HSLIPTG

pLas LasI LasRGFP

30C12HSL



ptet

TetRpLacIq

Circuit #3: atc->LasI Activator


UV 30C12HSLIPTG

pActivator LasI LasRGFP

30C12HSL



ptet

TetRpLacIqpLas Activator

atc

Circuit #4: Const. Lactonaseatc->LasR


UV 30C12HSLIPTG

pLas LasI GFP

30C12HSL



LasRptetTetRpLacIq

AiiApConstitutive

atc

Circuit #4A: Const. LactonaseNo atc


UV 30C12HSLIPTG

pLas LasI GFP

30C12HSL



LasRpLacIq AiiA

Circuit #5: atc->LactonasePositive Feedback LasI


UV 30C12HSLIPTG

pLas LasR GFP

30C12HSL



LasI

ptetTetRpLacIq AiiA

atc

Circuit #6: atc->Inducible LactonasePositive Feedback LasI


UV 30C12HSLIPTG

pLas LasR GFP

30C12HSL



LasI

pLas/tetOTetRpLacIq AiiA

atc

Null Null “1” “2”

Null versus 1 versus 2 Systems (Circuit #7)

NOTE: As before, not depicted is a stretch of DNA following the promoters and preceding the genes called the ‘RBS’. The RBS is tunable, thus controlling the strength of gene expression. Please account for this possibility.

Key: LasR has low sensitivity and only detects large circles (2) while RhiR system has high sensitivity for small circles (1). TetR represses small circles if when large are also present.

Operations: now we have two separate quorum sensing systems tuned to different sensitivities. To detect large circles, LasR will amplify with a low sensitivity. In the case where there is no large circle, a more sensitive RhiR system will detect and amplify a smaller circle. Forbidden bands in between each range are not unused by the digital input.

UV Toggle 3OC12HSL Quorum Sensor 3OC12HSL Propagator C4HSL Quorum Sensor C4HSL Propagator

State “1” = C4 ^ C12 State “2” = C12 Null = NOR(C4,C12)

Circuit #7: Null versus 1 versus 2 system


UV 30C12HSLIPTG

pLas LasI LasR BFP

30C12HSL

Quorum Sensors PropagatorToggle Switch

pRhiORI RhiI RhiR mCherry

C4HSL

pRhi RhiI RhiR GFP

C4HSL

Appendix

Following are circuit #1 with the Rhil and Lux systems. The same changes in promoters, inducers, and repressors can be applied to circuits #2-6.

Rhil System

CI pRhiORI RhiI RhiR mCherryLacI pLacpCI

UV C4HSLIPTG

pRhi RhiI RhiR GFP

C4HSL



Circuit #1

CI pLuxORI LuxI LuxR mCherryLacI pLacpCI

UV C6HSLIPTG

pLux LuxI LuxR GFP

C6HSL



Lux SystemCircuit #1

muri pattern detection circuits andrew yang, jonathan babb, ron weiss 9/23/2011

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