From 2007.igem.org

(Difference between revisions)

Revision as of 06:51, 26 October 2007

Wet Lab: DNA Constructs

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, Maxi, Mini, BL21	---	Cell By Date concept 1
	11	BBa_E7104	pT7 GFP	XL1, Maxi, Midi, Mini, BL21	---	Cell By Date concept 2
	30	---	pT7 (strong GFP)	XL1, Maxi, Mini, BL21	---	Construct to test T7 promoter
	18	BBa_T9002	ptet-luxR-plux-GFP	XL1, Maxi, Midi, BL21	---	Infector Detector construct 1

	05	BBa_R0040	ptet	XL1, Midi, Mini	DsRedEx	Cell By Date concept 1 with visual reporter
		BBa_I719005	pT7	Midi	DsRedEx	Cell By Date concept 2
	07	BBa_F2620	ptet-luxR-plux	XL1, Midi, Mini	DsRedEx	Infector Detector construct 1 with visual reporter

	21	BBa_J23039	ptet-luxI	XL1, Midi	---	AHL sender construct
	24	BBa_R0062	plux	XL1, Midi	DsRedEx	Infector Detector construct 2 with visual reporter
	25	BBa_J37032	plux-GFP	XL1, Maxi, Midi	---	Infector Detector construct 2

	13	BBa_B0015	Double terminator	XL1, Maxi, Midi, Mini	---	General part construction
	17	BBa_I13507	RFP	XL1, Midi	---	Not being used anymore
	19	BBa_B0034	strong RBS	XL1	---	General part construction
	23	BBa_I13504	GFP	XL1, Maxi, Midi	pT7	General part construction

		BBa_I719???	DsRed Express	Ordered	ptet, plux, pT7	Reporter system for ID, Hrp
		BBa_I719???	HrpR-HrpS	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_I719???	pT7 & GFP	Planned	pT7 + BBa_I13504	CBD test construct (pT7)

		BBa_I719???	DsRedEx & pSB1A3	Paused	DsRedEx + BBa_P1010	Biobrick Submission

		BBa_I719???	pT7 & DsRedEx	Planned	pT7 + DsRedEx	CBD final construct (pT7)
		BBa_I719???	ptet & DsRedEx	Planned	BBa_R0040 + DsRedEx	CBD final construct (ptet)
		BBa_I719???	ptet-luxR-plux-DsRedEx	Planned	BBa_F2620 + DsRedEx	ID detector final construct 1
		BBa_I719???	plux-DsRedEx	Planned	BBa_R0062 + DsRedEx	ID detector final construct 2

Legend: I (Information), [Status: XL1 - cloned in XL1-Blue; Maxi - maxiprepped; Midi - midiprepped; Mini - miniprepped; BL21 - cloned in BL21(DE3); status - stocks running low]

Parts from the Registry

Physical information of biobricks:

A

W

G

S

ID

Name

Description

Plasmid

Resist

Copy

Size(B)

Size(T)

Location

Conc.
(ng/ul)

A

W

G

02

BBa_I13522

GFP under tetracyclin promoter

pSB1A2

AmpR

High

937bp

3016bp

Well 15H, Plate 2

500

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

100/70

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

460

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

120/330

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

125/330

W

30

---

T7 with GFP(strong)

---

Kan?

???

---

???

---

150

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 Express 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
	W	14	BBa_R0051	pcI	pSB1A2	49bp	Biobrick	pcI 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
	W	20	---	AraC	pSB1AC3	1095bp	Planned	araC construct abandoned
A		26	BBa_S03119	ptet-LuxR	pSB1A2	XL1, Midi }} 998bp	not used in design
A		27	pSB1A3	pSB1A3	pSB1A3	failed-XL1	2157bp	biobrick not present
A	W	28	BBa_P1010	pSB1A3 (ccd)	pSB1A3	0bp	failed-XL1	Strain not available
A	W	29	BBa_P1010	pSB1A2 (ccd)	pSB1A2	0bp	---	Strain not available

@@ Line 21: / Line 21: @@
 <!-- PROMOTERS WITH GFP -->
 |- style="background:#CCFFFF" align="center"
-||  || 02 || [http://partsregistry.org/Part:BBa_I13522 BBa_I13522] || ptet-GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#00CC00>''Mini''</font>, <font color=#FF6633>BL21</font> || --- || Basic construct for chassis characterization
+||  || 02 || [http://partsregistry.org/Part:BBa_I13522 BBa_I13522] || ptet-GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#00CC00>''Mini''</font>, <font color=#FF6633>BL21</font> || --- || [[Imperial/Cell_by_Date/Design#DNA_Constructs|Cell By Date concept 1]]
 |- style="background:#CCFFFF" align="center"
-||  || 11 || [http://partsregistry.org/Part:BBa_E7104 BBa_E7104] || pT7 GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF><small>''Maxi''</small></font>,  <font color=#0000FF>''Midi''</font>, <font color=#00CC00>''Mini''</font>, <font color=#FF6633>BL21</font> || --- || CBD test construct (pT7)
+||  || 11 || [http://partsregistry.org/Part:BBa_E7104 BBa_E7104] || pT7 GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF><small>''Maxi''</small></font>,  <font color=#0000FF>''Midi''</font>, <font color=#00CC00>''Mini''</font>, <font color=#FF6633>BL21</font> || --- || [[Imperial/Cell_by_Date/Design#DNA_Constructs|Cell By Date concept 2]]
 |- style="background:#CCFFFF" align="center"
-||  || 30 || --- || pT7 (strong GFP) ||  <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#00CC00>''Mini''</font>, <font color=#FF6633>BL21</font>|| --- || T7 test-construct
+||  || 30 || --- || pT7 (strong GFP) ||  <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#00CC00>''Mini''</font>, <font color=#FF6633>BL21</font>|| --- || Construct to test T7 promoter
 |- style="background:#CCFFFF" align="center"
-|| [[IGEM:IMPERIAL/2007/DNA_Constructs/BBa_J24677|I]] || 18 || [http://partsregistry.org/Part:BBa_T9002 BBa_T9002] || ptet-luxR-plux-GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#0000FF><small>''Midi''</small></font>, <font color=#FF6633>BL21</font> || --- || Basic construct for chassis characterization
+||  || 18 || [http://partsregistry.org/Part:BBa_T9002 BBa_T9002] || ptet-luxR-plux-GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#0000FF><small>''Midi''</small></font>, <font color=#FF6633>BL21</font> || --- || [[Imperial/Infector_Detector/Design#DNA_Constructs|Infector Detector construct 1]]
 |- style="background:#CCFFFF" align="center"
@@ Line 36: / Line 36: @@
 <!-- PROMOTERS ONLY -->
 |- style="background:#CCFFFF" align="center"
-||  || 05 || [http://partsregistry.org/Part:BBa_R0040 BBa_R0040] || ptet || <font color=#CC0000>XL1</font>, <font color=#0000FF>''Midi''</font>, <font color=#00CC00>''Mini''</font> || DsRedEx || CBD final (ptet), ID AHL sender
+||  || 05 || [http://partsregistry.org/Part:BBa_R0040 BBa_R0040] || ptet || <font color=#CC0000>XL1</font>, <font color=#0000FF>''Midi''</font>, <font color=#00CC00>''Mini''</font> || DsRedEx || [[Imperial/Cell_by_Date/Design#DNA_Constructs|Cell By Date concept 1]] with visual reporter
 |- style="background:#CCFFFF" align="center"
-||  ||  || BBa_I719??? || pT7 || ''Ready'' || DsRedEx || CBD final construct (pT7)
+||  ||  || [http://partsregistry.org/Part:BBa_I719005 BBa_I719005] || pT7 || <font color=#0000FF>''Midi''</font> || DsRedEx || [[Imperial/Cell_by_Date/Design#DNA_Constructs|Cell By Date concept 2]]
 |- style="background:#CCFFFF" align="center"
-||  || 07 || [http://partsregistry.org/Part:BBa_F2620 BBa_F2620] || ptet-luxR-plux || <font color=#CC0000>XL1</font>, <font color=#0000FF>''Midi''</font>, <font color=#00CC00>''Mini''</font> || DsRedEx || ID final construct
+||  || 07 || [http://partsregistry.org/Part:BBa_F2620 BBa_F2620] || ptet-luxR-plux || <font color=#CC0000>XL1</font>, <font color=#0000FF>''Midi''</font>, <font color=#00CC00>''Mini''</font> || DsRedEx || [[Imperial/Infector_Detector/Design#DNA_Constructs|Infector Detector construct 1]] with visual reporter
 |- style="background:#CCFFFF" align="center"
@@ Line 48: / Line 48: @@
 <!-- ID SPECIFIC BRICKS -->
 |- style="background:#CCFFFF" align="center"
-||  || 21 || [http://partsregistry.org/Part:BBa_J23039 BBa_J23039] || ptet-luxI || <font color=#CC0000>XL1</font>, <font color=#0000FF><small>''Midi''</small></font> || --- || ID sender construct
+||  || 21 || [http://partsregistry.org/Part:BBa_J23039 BBa_J23039] || ptet-luxI || <font color=#CC0000>XL1</font>, <font color=#0000FF><small>''Midi''</small></font> || --- || AHL sender construct
 |- style="background:#CCFFFF" align="center"
-||  || 24 || [http://partsregistry.org/Part:BBa_R0062 BBa_R0062] || plux || <font color=#CC0000>XL1</font>, <font color=#0000FF>''Midi''</font> || DsRedEx || ID construct 2
+||  || 24 || [http://partsregistry.org/Part:BBa_R0062 BBa_R0062] || plux || <font color=#CC0000>XL1</font>, <font color=#0000FF>''Midi''</font> || DsRedEx || [[Imperial/Infector_Detector/Design#DNA_Constructs|Infector Detector construct 2]] with visual reporter
 |- style="background:#CCFFFF" align="center"
-||  || 25 || [http://partsregistry.org/Part:BBa_J37032 BBa_J37032] || plux-GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#0000FF>''Midi''</font> || --- || ID construct 2
+||  || 25 || [http://partsregistry.org/Part:BBa_J37032 BBa_J37032] || plux-GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#0000FF>''Midi''</font> || --- || [[Imperial/Infector_Detector/Design#DNA_Constructs|Infector Detector construct 2]]
-|- style="background:#CCFFFF" align="center"
-||  || 26 || [http://partsregistry.org/Part:BBa_S03119 BBa_S03119] || ptet-luxR || <font color=#CC0000>XL1</font>, <font color=#0000FF>''Midi''</font> || --- || ---
-|- style="background:#CCFFFF" align="center"
-||  ||  ||  ||  ||  ||  ||
 <!-- BRICKS WITH PLASMID VECTORS -->
-|- style="background:#CCFFFF" align="center"
+<!-- there are none of there : (-->
-||  || 27 || [http://partsregistry.org/Part:pSB1A3 pSB1A3] || Empty pSB1A3 || '''Problematic''' || --- || ---
 |- style="background:#CCFFFF" align="center"
@@ Line 195: / Line 189: @@
 |- style="background:#FFCCFF" align="center"
 || A ||  || G ||  || 25 || [http://partsregistry.org/Part:BBa_J37032 BBa_J37032] || GFP under lux promoter || [http://partsregistry.org/Part:pSB1A2 pSB1A2] || AmpR || High || 938bp || 3017bp || Well 8D, Plate 3 || 125/330
-|- style="background:#FFCCFF" align="center"
-|| A ||  || G ||  || 26 || [http://partsregistry.org/Part:BBa_S03119 BBa_S03119] || constitutive LuxR || [http://partsregistry.org/Part:pSB1A2 pSB1A2] || AmpR || High || 998bp || 3077bp || Well 19J, Plate 1 || 60
-|- style="background:#FFCCFF" align="center"
-|| A || W || <font color=#990033>X</font> ||  || 27 || [http://partsregistry.org/Part:pSB1A3 pSB1A3] || pSB1A3 (blank) || [http://partsregistry.org/Part:pSB1A3 pSB1A3] || Amp || High || 0bp || 2157bp || Well 23E, Plate 1 || --
 |- style="background:#FFCCFF" align="center"
@@ Line 291: / Line 279: @@
 |- style="background:#DDDDDD" align="center"
 ||  || W || 20 || --- || AraC || pSB1AC3 || 1095bp || Planned || araC construct abandoned
+|- style="background:#DDDDDD" align="center"
+|| A ||  || 26 || BBa_S03119 || ptet-LuxR || pSB1A2 || XL1, Midi }} 998bp || not used in design
+|- style="background:#DDDDDD" align="center"
+|| A ||  || 27 || pSB1A3 || pSB1A3 || pSB1A3 || failed-XL1 || 2157bp || biobrick not present
 |- style="background:#DDDDDD" align="center"

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Imperial/Wet Lab/DNA Constructs

From 2007.igem.org

Revision as of 06:51, 26 October 2007

Wet Lab: DNA Constructs

Constructs Overview

Cloning Table

Ligation Table

Parts from the Registry

Our Parts

Part Graveyard