IGEM:IMPERIAL/2007/DNA Constructs

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==Constructs Overview==
==Constructs Overview==
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Here are several tables listing the bricks which we are cloning, constructing and using, with their relevant details.
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===Cloning Table===
===Cloning Table===
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Status of biobricks cloned and their applications:
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||  ||  || BBa_I719??? || HrpR-HrpS-pHrpL || Ordered || ??? || Hrp core system
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||  ||  || BBa_I719??? || HrpR-HrpS-pHrpL || Ordered || ??? || Hrp regulators
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||  ||  || BBa_I719??? || pHrpL || Ordered || ??? || Hrp promoter
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===Ligation Table===
===Ligation Table===
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Status of parts ligated and their applications:
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===Parts from the Registry===
===Parts from the Registry===
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Physical information of biobricks:
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|| A || W || <font color=#339900>G</font> ||  || 11 || [http://parts.mit.edu/registry/index.php/Part:BBa_E7104 BBa_E7104] || T7 GFP|| [http://parts.mit.edu/registry/index.php/Part:pSB1A2 pSB1A2] || AmpR || High || 826bp || 2905bp || Well 13F, Plate 2  || 100
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|| A || <font color=#990033>X</font> || <font color=#339900>G</font> ||  || 11 || [http://parts.mit.edu/registry/index.php/Part:BBa_E7104 BBa_E7104] || T7 GFP|| [http://parts.mit.edu/registry/index.php/Part:pSB1A2 pSB1A2] || AmpR || High || 826bp || 2905bp || Well 13F, Plate 2  || 100
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===Our Parts===
===Our Parts===
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Physical information of our ligated parts:
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<font size="-2">Legend: A (Available), W (Working) [<font color=#00CC00>W</font> - working ''in vivo'', <font color=##0000FF>W</font> - working ''in vitro''], G (Checked on gel) [<font color=#339900>G</font> - incorrect size; <font color=#990033>X</font> - does not appear on gel], S (Sequenced)<br>Concentrations are given in ng/μl</font>
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<font size="-2">Legend: A (Available), W (Working) [<font color=#00CC00>W</font> - working ''in vivo'', <font color=##0000FF>W</font> - working ''in vitro'', <font color=#990033>X</font> - faulty], G (Checked on gel) [<font color=#339900>G</font> - incorrect size; <font color=#990033>X</font> - does not appear on gel], S (Sequenced)<br>Concentrations are given in ng/μl</font>
===Part Graveyard===
===Part Graveyard===
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General information on parts we do not like...
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==Construct Diagrams==
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The original (old) diagrams page was moved to [[IGEM:IMPERIAL/2007/DNA_Constructs/Con_Diagrams_old|old construct diagrams]] page.
==Constructs for Cell By Date==
==Constructs for Cell By Date==

Revision as of 14:53, 30 August 2007

Contents

Constructs Overview

Here are several tables listing the bricks which we are cloning, constructing and using, with their relevant details.

Cloning Table

Status of biobricks cloned and their applications:

I ID Part Description Status Ligation Target Use in Constructs
02 BBa_I13522 ptet-GFP XL1, Midi, Mini, BL21 --- Basic construct for chassis characterization
11 BBa_E7104 pT7 GFP XL1, Midi, Mini, BL21 --- CBD test construct (pT7)
I 18 BBa_T9002 ptet-luxR-plux-GFP XL1, Midi, BL21 --- Basic construct for chassis characterization
05 BBa_R0040 ptet XL1, Midi, Mini DsRed CBD final (ptet), ID AHL sender
BBa_I719??? pT7 Pending DsRed CBD final construct (pT7)
07 BBa_F2620 ptet-luxR-plux XL1, Midi, Mini DsRed ID final construct
14 BBa_R0051 pcI Problematic DsRed CBD final construct (pcI)
21 BBa_J23039 ptet-luxI XL1, Midi --- ID sender construct
24 BBa_R0062 plux XL1, Midi --- ID construct 2
25 BBa_J37032 plux-GFP XL1, Midi --- ID construct 2
26 BBa_S03119 ptet-luxR XL1, Midi --- ---
13 BBa_B0015 Double terminator XL1, Midi, Mini --- General part construction
17 BBa_I13507 RFP XL1, Midi --- Not being used anymore
19 BBa_B0034 strong RBS XL1, Waiting Midi --- General part construction
23 BBa_I13504 GFP XL1, Midi pcI General part construction
BBa_I719??? DsRed Ordered ptet, plux, pcI Reporter system for ID, Hrp
BBa_I719??? HrpR-HrpS-pHrpL Ordered  ??? Hrp regulators
BBa_I719??? pHrpL Ordered  ??? Hrp promoter
BBa_I719??? HrpV Ordered  ??? Hrp inhibitor system

Ligation Table

Status of parts ligated and their applications:

I ID Part Description Status Parents Application
BBa_I719021 ptet & luxI Paused R0040 + F1610 ID final sender (duplicated - J23039)
BBa_I719022 pcI & GFP Planning BBa_R0051 + BBa_I13504 CBD test construct (pcI)
BBa_I719??? pT7 & DsRed Pending pT7 + DsRed CBD final construct (pT7)
BBa_I719??? ptet & DsRed Pending BBa_R0040+ DsRed CBD final construct (ptet)
BBa_I719??? pcI-DsRed Pending BBa_R0051 + DsRed CBD final construct (pcI)
BBa_I719??? ptet-luxR-plux-DsRed Pending BBa_F2620 + DsRed ID detector final construct
BBa_I719??? hrpR-hrpS & phrpL Pending hrpR-hrpS + phrpL ID detector test construct 3 and final construct 5
BBa_I719??? Ptet-luxR-Plux & hrpR-hrpS-phrpL Pending BBa_F2620 + hrpR-hrpS-phrpL ID detector test construct 3 and final construct 5
BBa_I719??? Ptet-luxR-Plux-hrpR-hrpS-phrpL & GFP Pending Ptet-luxR-Plux-hrpR-hrpS-phrpL + BBa_E0240 ID detector test construct 3
BBa_I719??? Ptet-luxR-Plux-hrpR-hrpS-phrpL & DsRed Pending Ptet-luxR-Plux-hrpR-hrpS-phrpL + DsRed ID detector final construct 5

Legend: I (Information), [Status: XL1 - cloned in XL1-Blue; Midi - midiprepped; Mini - miniprepped; BL21 - cloned in BL21(DE3)]

Parts from the Registry

Physical information of biobricks:

A W G S ID Name Description Plasmid Resist Copy Size(B) Size(T) Location Conc.
A W G 02 BBa_I13522 GFP under tetracyclin promoter pSB1A2 AmpR High 937bp 3016bp Well 15H, Plate 2 110/100
A W G 05 BBa_R0040 tetracyclin promoter pSB1A2 AmpR High 54bp 2133bp Well 7O, Plate 1 60
A W G 07 BBa_F2620 lux promoter, with luxR pSB1A2 AmpR High 1061bp 3140bp Well 6B, Plate 1 80
A X G 11 BBa_E7104 T7 GFP pSB1A2 AmpR High 826bp 2905bp Well 13F, Plate 2 100
A W G 13 BBa_B0015 Double terminator pSB1AK3 A+KR High 129bp 3316bp Well 1B, Plate 2 100
W X 14 BBa_R0051 λcI promoter pSB1A2 AmpR High 49bp 2128bp Well 9C, Plate 1 --
A G 17 BBa_I13507 RFP pSB1A2 AmpR High 861bp 2940bp Well 16N, Plate 1 80
A W G 18 BBa_T9002 GFP under lux promoter with LuxR pSB1A3 AmpR High 1945bp 4102bp Well 19B, Plate 2 100
A W 19 BBa_B0034 RBS pSB1A2 AmpR High 12bp 2091bp Well 3O, Plate 1 --
A G 21 BBa_J23039 Constitutive luxI pSB1A2 AmpR High 860bp 2939bp Well 11K, Plate 3 140
A W G 23 BBa_I13504 GFP pSB1A2 AmpR High 875bp 2954bp Well 16E, Plate 1 120
A G 24 BBa_R0062 lux promoter pSB1A2 AmpR High 55bp 2134bp Well 9G, Plate 1 90
A G 25 BBa_J37032 GFP under lux promoter pSB1A2 AmpR High 938bp 3017bp Well 8D, Plate 3 100
A G 26 BBa_S03119 constitutive LuxR pSB1A2 AmpR High 998bp 3077bp Well 19J, Plate 1 60

Our Parts

Physical information of our ligated parts:

A W G S ID Name Description Plasmid Resist Copy Size(B) Size(P) Stock
BBa_I719022 cI with GFP pSB1A2 AmpR High 933bp 3988bp
BBa_I791021 luxI coding region under ptet pSB1A2 AmpR High 860bp 2939bp
BBa_I791??? DsRed under ptet pSB1A2 AmpR High

Legend: A (Available), W (Working) [W - working in vivo, W - working in vitro, X - faulty], G (Checked on gel) [G - incorrect size; X - does not appear on gel], S (Sequenced)
Concentrations are given in ng/μl

Part Graveyard

General information on parts we do not like...

A W ID Name Description Plasmid Size Status Notes
A W 01 BBa_E0040 GFP pSB1A2 720bp XL1, Mini Redundant
A 03 BBa_J5528 pBad-GFP pSB2K3 2093bp failed-XL1 ara construct abandoned
A 04 BBa_J24677 plux-GFP pSB1A2 1787bp XL1, Mini Wrong GFP ligated
A 06 BBa_I0500 pBad pSB2K3 1210bp XL1, Mini, Midi ara construct abandoned
A W 08 BBa_F1610 luxI pSB1AK3 798bp XL1, Mini, Midi Substitute part J23039
A W 09 BBa_R0010 lacI-plac pSB1A2 200bp XL1, Mini Lac construct abandoned
A W 10 BBa_E1010 RFP pSB2K3 681bp XL1, Mini Substitute part I13507
A 12 BBa_S03550 araC pSB1AC3 958bp XL1, Mini, Midi araC construct abandoned
A 15 BBa_J07037 cI-GFP pSB2K3 912bp XL1, Mini No RBS present on this part
A W 16 BBa_E0240 GFP pSB1A2 876bp XL1, Midi Redundant
20 --- AraC pSB1AC3 1095bp Planned araC construct abandoned


Construct Diagrams

The original (old) diagrams page was moved to old construct diagrams page.

Constructs for Cell By Date

  • Construct CBD 1
    • Entire construct is currently available in Biobricks Registry: BBa_E7104 (available), in pSB1A2 (AmpR)
    • pT7 can be used with T7 RNAP in vitro and in veso, and it gives constitutive expression.
PT7 promoting GFP
PT7 promoting GFP

  • Construct CBD 2
    • Entire construct is currently in Biobricks Registry: BBa_I13522 (available), in pSB1A2 (AmpR)
    • pTet can be used with E.coli RNAP in vitro and maybe in veso, and it gives constitutive expression.
Ptet promoting GFP
Ptet promoting GFP

  • Construct CBD 3
    • pBAD promoter with GFP is currently available in Biobricks Registry: BBa_J5528 (available), in pSB2K3 (KanR)
    • Need Ara C regulator protein in vitro and in veso. Ara C available with the RBS:BBa_S03550
    • pBad can be used with E.coli RNAP in vitro, and it is inducible by arabinose.
    • To be used in veso, arabinose transport proteins have to be inserted in the phospholipid bilayer of the vesicles.
PBAD promoting GFP and Ptet promoting araC
PBAD promoting GFP and Ptet promoting araC

  • Construct CBD 4
    • Entire construct is currently available in Biobricks Registry: BBa_J07037 (avaiable), in pSB2K3 (KanR)
    • pcI gives constitutive expression.
PcI promoting GFP
PcI promoting GFP

PBAD promoting GFP and PcI promoting araC
PBAD promoting GFP and PcI promoting araC

  • Construct CBD 6
    • T7 promoter is in the process of cloning
    • dsRed has been ordered
pT7 promoting dsRed
pT7 promoting dsRed

  • Construct CBD 7
    • tet promoter available in the registry: BBa_R0040
    • dsRed has been ordered
Ptet promoting dsRed
Ptet promoting dsRed


  • Construct CBD 8
PBAD promoting RFP and Ptet promoting araC
PBAD promoting RFP and Ptet promoting araC


  • Construct CBD 9
    • λcI regulated promoter available in the registry:BBa_R0051
pcI promoting RFP
pcI promoting RFP


  • Construct CBD 10
    • Parts avaiable ....
PBAD promoting RFP and PcI promoting araC
PBAD promoting RFP and PcI promoting araC


Constructs for Infector Detector

  • Construct ID 1
    • Entire part minus promoter is currently in Biobricks Registry: BBa_F1610 (available), in pSB1AK3 (AmpR, KanR)
    • pTet is currently in Biobricks Registry: BBa_R0040 (available), in pSB1A2 (AmpR)
    • pTet can be used with E.coli RNAP in vitro and maybe in veso, and it gives constitutive expression.
Ptet promoting LuxI
Ptet promoting LuxI

  • Construct ID 2
    • Entire part is currently in Biobricks Registry: BBa_J24677 (available), in pSB1A2 (AmpR)
    • Entire part minus GFP reporter system is currently in Biobricks Registry: BBa_F2620 (available), in pSB1A2 (AmpR)
    • GFP reporter system is currently in Biobricks Registry: BBa_I13504 (available)
    • pLux can be used with E.coli RNAP in vitro and maybe in veso, and it is repressed by LuxR but activated by AHL:LuxR complex.
Ptet promoting LuxR, Plux promoting GFP
Ptet promoting LuxR, Plux promoting GFP

  • Construct ID 3
    • Entire part minus Hrp system is currently in Biobricks Registry: BBa_F2620(available) in pSB1A2 (AmpR)
    • pHrpL can be used with E.coli RNAP in vitro and maybe in veso, and it is inducible by HrpR:HrpS:Sigma 54 complex.
Ptet promoting LuxR, Plux promoting HrpR and HrpS and PHrpL promoting GFP
Ptet promoting LuxR, Plux promoting HrpR and HrpS and PHrpL promoting GFP

  • Construct ID 4
    • Entire part minus dsRed reporter system is currently in Biobricks Registry: BBa_F2620 (available), in pSB1A2 (AmpR)
    • dsRed has been ordered
Ptet promoting LuxI
Ptet promoting LuxI

  • Construct ID 5
    • Entire part minus the hrp system and dsRed reporter system is currently in Biobricks Registry: BBa_F2620 (available), in pSB1A2 (AmpR)
    • dsRed has been ordered
    • hrpR-hrpS-pHrpL has been ordered
Ptet promoting LuxR, Plux promoting HrpR and HrpS and PHrpL promoting lacZ
Ptet promoting LuxR, Plux promoting HrpR and HrpS and PHrpL promoting lacZ

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