From 2010.igem.org

(Difference between revisions)

Latest revision as of 18:08, 27 October 2010

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Project Overview

Speedy reporter

Speedy switch

Speedy protein degrader

Experiments and Parts

Applications

F.A.Q

About Us

Our Goal

GFP

Purpose

Insert lva tag to the GFP by using PCR and ligate to pLac.

Material

[http://partsregistry.org/Part:BBa_R0010 BBa_R0010]: pLac

[http://partsregistry.org/Part:BBa_E0240 BBa_E0240]: RBS([http://partsregistry.org/Part:BBa_B0034 BBa_B0034]) +GFP([http://partsregistry.org/Part:BBa_E0040 BBa_E0040]) +Terminator([http://partsregistry.org/Part:BBa_B0015 BBa_B0015])

Parts Length

DNA Length
Part	Part Length	Length in pSB1A2
E0240	876bp	1114bp
E0240+LVA	909bp	1147bp
R0010+E0240+LVA	1117bp	1355bp

RFP

Purpose

Insert lva tag to the RFP by using PCR and ligate to pLac.

Material

BBa_R0010:pLac

[http://partsregistry.org/Part:BBa_I13507 BBa_I13507]: RBS(BBa_B0034)+RFP([http://partsregistry.org/Part:BBa_E1010 BBa_E1010])+Terminator(BBa_B0015)

Parts Length

DNA Length
Part	Part Length	Length in pSB1A2
I13507	861bp	1099bp
I13507+LVA	894bp	1132bp
R0010+I13507+LVA	1102bp	1340bp

CFP

Purpose

1.After ligate CFPlva to Terminator and RBS , ligate to pLac.

2.Remove LVA from the sequences to construct the control.

Material

BBa_R0010: pLac

BBa_B0034: RBS

[http://partsregistry.org/Part:BBa_E0022 BBa_E0022]: CFPlva

BBa_B0015: Terminator

Parts Length

DNA Length
Part	Part Length	Length in pSB1A2
E0022	762bp	1000bp
E0022+B0015	899bp	1137bp
B0034+E0022+B0015	919bp	1157bp
R0010+B0034+E0022+B0015	1127bp	1365bp

YFP

Purpose

1.After ligate YFPlva to Terminator and RBS , ligate to pLac.

2.Remove LVA from the sequences to construct the control.

Material

BBa_R0010: pLac

BBa_B0034: RBS

[http://partsregistry.org/Part:BBa_E0032 BBa_E0032]: YFPlva

BBa_B0015: Terminator

Parts Length

DNA Length
Part	Part Length	Length in Plasmid
E0032	762bp	1000bp
E0032+B0015	899bp	1137bp
B0034+E0032+B0015	919bp	1157bp
R0010+B0034+E0032+B0015	1127bp	1365bp

Our Experiment Data

2010-07-22

1. Extract B0034(RBS) from 2010 plate 1 2U

Extract B0015(Terminator) from 2010 plate 1 23L

2.Transform into 15ul competent cells.

3.Add 85ul LB after heat shock.

4.Culture for 30 minutes.

5.80ul for transformation ; 20ul for liquid culture

6.Incubate at 6:00pm.

2010-07-23

1.Extract RBS and Term(abbreviation for terminator) cultured in 7/22.

2.Measured the nano drop.

B0015:26.94ng/ul
B0034:45.59ng/ul

3.Digest B0034(SP) and B0015(XP) at 11:30am

4.Run the gel for B0015.

5.Measured the nano drop.

B0034:3.85ng/ul

6.Purify B0034.

7.Ligate YFPlva and CFPlva to Term.

8.Transform into 30ul competent cells.

9.PCR to make GFPlva and RFPlva front parts.

2010-07-24

1.Do 3 in 1 and PCR to check CFPlva+Terminator ,YFPlva+Terminator ,RBS , Terminator.

2.Run the gel.

3.PCR to make the whole parts GFPlva and RFPlva.

4.Run the gel.

5.Digest GFPlva(XP) and RFPlva(XP).

6.Measure the nano drop.

GFPlva:8.66ng/ul
RFPlva:7.35ng/ul

7.Ligate GFPlva and RFPlva to psB1A2.

8.Tranform into 30ul competent cells.

2010-07-26

1.Digest RBS(SP), CFP(XP), YFP(XP) and Term(P)

2.Run the gel for .

3.Digest CFPlva and YFPlva.

4.Ligate CFPlva and YFPlva to Term.

2010-07-28

1.Do 3 in 1 to check GFPlva ,RFPlva , YFPlva+Term and CFPlva+Term.

2.Run the gel.

2010-07-29

1.Extract GFPlva and RFPlva cultured on 7/29.

2.Digest GFPlva(X,NdeI) and RFPlva(X,NcoI) for checking if they were correct. Digest YFPlva(E) ,CFPlva(E) and Term(E) for ligation.

3.After 10 minutes ,degrade EcoRI by rising the temperature to 80 for 5 minutes.

4.Run the gel for YFPlva ,CFPlva and Term and purify them.

5.Digest YFPlva(ES) ,CFPlva(ES) and Term(EX).

6.Measure the nano drop.

7.Run the gel for YFPlva(ES) ,CFPlva(ES) ,Term(EX) ,GFPlva and RFPlva.

8.Ligate CFPlva(ES) and YFPlva(ES) to Term(EX).

9.PCR the whole part for GFPlva and RFPlva again.

2010-07-31

1.Do 3 in 1 for YFPlva+Term and CFPlva+Term.

2.Run the gel for YFPlva+Term ,CFPlva+Term ,RFPlva and GFPlva.

3.Ligate YFPlva(ES) to Term(EX).

4.PCR the front part of GFPlva and RFPlva for checking the condition is right or wrong.

5.Run the gel to make the front part of GFPlva and RFPlva.

2010-08-02

1.Do 3 in 1 for YFPlva+Term.

2.Digaest CFPlva+Term ,RBS(SP) ,Term(ES) and Term(E).

3.Measure the nano drop.

4.PCR to make the front part of GFPlva and RFPlva.

5.Ligate RBS(SP) to CFPlva+Term (XP).

6.Liquid culture for RBS.

2010-08-04

1.PCR to make the whole part of GFPlva and RFPlva.

2.Extract GFPlva ,RFPlva ,YFPlva+Term ,RBS.

2010-08-05

1.PCR for RFPlva, GFP without RBS, RFP without RBS, RBS+YFP+term, GFPlva.

2.Run gel for RBS+YFP+term, GFPlva, RFPlva, GFP without RBS, RFP without RBS

2010-08-06

1.PCR for front part of GFP without RBS and front part of RFP without RBS

2.Extraction for YFP, GFPlva, RFPlva

3.Digestion

4.Run gel for RBS+YFP+term

5.PCR again for GFP without RBS, RFP without RBS

6.Purification for YFP, GFPlva, RFPlva

7.Nanodrop

GFPlva(XP)     3.89ng/uL
RFPlva(XP)     4.48ng/uL
RBS+YFP+term   3.18ng/uL

8.Ligate CFP+term with RBS

9.Transformation

2010-08-07

1.Colony PCR for RBS+CFP+Term, GFP, RFP

2.Run gel for RBS+CFP+term, GFP, RFP

2010-08-09

1.Extraction for GFP, RFP

2.Colony PCR for GFP

2010-08-10

1.Digestion for GFPlva(XP), YFPlva(XP), RFPlva(XP), CFP+Term(XP)

2.Run gel for GFPlva(XP), YFPlva(XP), RFPlva(XP), CFP+Term(XP)

2010-08-11

1.Extract CFP+term

2.Real PCR for GFP wihout RBS, RFP without RBS

3.Ligate RBS with CPF+Term

4.Transform RBS with CPF+Term, pLac(R0010)

2010-08-12

1.Colony PCR for RBS+CFP+Term, pLac

2.Run gel for GFP without RBS, RFP without RBS, pLac

2010-08-14

1.Extract pLac

2.Digest pLac(SP)

3.Nanodrop

pLac1     5.73ng/uL
pLac2     2.70ng/uL
pLac3     4.08ng/uL

2010-08-17

1.Ligate RBS with CFP+term

2.Transform RBS with CFP+term

3.Digest GFPlva(XP), RBS+YFPlva+term(XP)

4.Run gel for GFPlva(XP), RBS+YFPlva+term(XP)

5.Purify GFPlva(XP), RBS+YFPlva+term(XP)

6.Nanodrop

GFPlva(XP)           8.87 ng/uL
RBS+YFPlva+term(XP)     5.01 ng/uL

7.Culture GFPlva, RBS+YFPlva+term

2010-08-18

1.Extract GFPlva, RBS+YFPlva+term

2.Digest RBS, CFP+term

3.Ligate CFP+term with RBS

2010-08-19

1.Colony PCR for RBS+CFPlva+Term

2.Nanodrop

 RBS(SP)        21.38ng/uL
 CFP+Term(XP)   10.38ng/uL

3.Run gel for RBS+CFPlva+Term

4.Ligate RBS with CFPlva+term

5.Transform

2010-08-20

1.Colony PCR for RBS+CFPlva+term

2.Run gel for RBS+CFPlva+term

2010-08-21

1.Extract for RFP+CFPlva+term

2.Digest RBS+CFPlva+term(XP), RBS(SP)

3.Run gel for RBS+CFPlva+term

4.Purify RBS+CFPlva+term(XP), RBS(SP)

5.Nanodrop

 RBS1                  2.96 ng/uL
 RBS2                  2.02 ng/uL
 RBS+CFPlva+term       8.98 ng/uL

2010-08-23

1.Ligate pLac with RBS+GFPlva+term, pLac with RBS+YFPlva+term, pLac with RBS+RFPlva+term

2.Transform pLac with RBS+GFPlva+term, pLac with RBS+YFPlva+term, pLac with RBS+RFPlva+term

2010-08-24

1.Colony PCR for pLac+RBS+GFPlva+term, pLac+RBS+YFPlva+term, pLac+RBS+RFPlva+term

2010-09-01

1.Colony PCR for pLac+RBS+GFPlva+term

2.Extract RBS+CFPlva+term

3.Digest RBS+CFPlva+term(XP)

4.Run the gel for pLac+RBS+GFPlva+term,RBS+CFPlva+term(XP)

5.Ligate pLac with RBS+GFPlva+term, pLac wtih RBS+RFPlva+term, pLac with RBS+YFPlva+term, pLac with RBS+CFPlva+term

2010-09-02

1.Colony PCR for pLac+RBS+GFPlva+term, pLac+RBS+RFPlva+term, pLac+RBS+YFPlva+term, pLac+RBS+CFPlva+term

2.Run gel for pLac+RBS+GFPlva+term, pLac+RBS+RFPlva+term, pLac+RBS+YFPlva+term, pLac+RBS+CFPlva+term

2010-09-04

1.Extract pLac+RBS+GFPlva+term, pLac+RBS+RFPlva+term, pLac+RBS+YFPlva+term, pLac+RBS+CFPlva+term

2.Digest pLac+RBS+GFPlva+term(XP), pLac+RBS+RFPlva+term(XP), pLac+RBS+YFPlva+term(XP), pLac+RBS+CFPlva+term(XP)

3.Run gel for pLac+RBS+GFPlva+term(XP), pLac+RBS+RFPlva+term(XP), pLac+RBS+YFPlva+term(XP), pLac+RBS+CFPlva+term(XP)

4.Purify pLac+RBS+GFPlva+term(XP), pLac+RBS+RFPlva+term(XP), pLac+RBS+YFPlva+term(XP), pLac+RBS+CFPlva+term(XP)

5.Nanodrop

pLac+RBS+GFPlva+term(XP)1           22.31 ng/uL
pLac+RBS+GFPlva+term(XP)2           14.16 ng/uL
pLac+RBS+RFPlva+term(XP)             8.6  ng/uL
pLac+RBS+YFPlva+term(XP)            13.52 ng/uL
pLac+RBS+CFPlva+term(XP)1           21.79 ng/uL
pLac+RBS+CFPlva+term(XP)2            7.87 ng/uL

2010-09-11

1.PCR to make the front part and back part of the YFP and CFP. (in order to remove lva tag)

2.Run the gel for the front part and back part of YFP and CFP.(load 5ul)

3.While running the gel ,we purified them.

4.After the gel result appeared ,run the gel for YFP and CFP which had been purified to extract the correct length.(load 20ul)

	template	forward primer	reverse primer
positive	RFP	VF2	VR
YFP front part	pLac+RBS+YFPlva+Term	VF2	XFP lva remover rp
YFP back part	pLac+RBS+YFPlva+Term	XFP lva remover fp	VR
CFP front part	pLac+RBS+CFPlva+Term	VF2	XFP lva remover rp
CFP back part	pLac+RBS+CFPlva+Term	XFP lva remover fp	VR

Extract the gel and purify them.

Extract pLac+GFPlva ,pLac+RBS+YFPlva+Term and pLac+RBS+CFPlva+Term.

Measure the nano drop.

pLac+GFPlva: 170.51ng/ul

pLac+RBS+YFPlva+Term: 276.08ng/ul

pLac+RBS+YFPlva+Term: 287.46ng/ul

pLac+RBS+CFPlva+Term: 116.21ng/ul

pLac+RBS+CFPlva+Term: 252.12ng/ul

2010-09-18

1.Extract RFP.

2.Do the PCR to make the front part and back part of the RFPlva and to make the whole part of pLac+RBS+YFP+Term and pLac+RBS+YFP+Term.

2010-09-30

1.Run the gel for sspB, the front part of RBS+CFP+term, the front part of RBS+YFP+term, the front part of RBS+RFPlva+term, the back part of RBS+CFP+term, the back part of RBS+YFP+term, the back part of RFPlva and RFP

2.Purify sspB, the front part of RBS+CFP+term, the front part of RBS+YFP+term, the front part of RBS+RFPlva+term, the back part of RBS+CFP+term, the back part of RBS+YFP+term and RFP

3.Measure nanodrop

 sspB                                  34.73ng/uL
 the front part of RBS+CFP+term        15.82ng/uL
 the front part of RBS+YFP+term        35.53ng/uL
 the front part of RBS+RFPlva+term     76.10ng/uL
 the back part of RBS+CFP+term         34.89ng/uL
 the back part of RBS+YFP+term         36.27ng/uL
 RFP                                   79.82ng/uL

2010-10-1

1.PCR to make back part of RFPlva

2.Digest pLac(SP), sspB(PCR) and RFP(PCR)

2010-10-4

1.3-in-1 for pLac+RFP

2.Run the gel for pLac+RFP

2010-10-7

1.Extract RFPlva(PCR)

 RFPlva   100ng/uL

2.Digest RFPlva(XP)

2010-10-9

1.3-in-1 for K145205

2.PCR to make the whole part of pLac+RBS+YFP+term and pLac+RBS+CFP+term

3.Purify RFP(PCR)(XP)

 Nanodrop:
 RFP           42.3ng/uL

4.Ligate pLac(SP)+RBS+RFP+term(PCR)(XP)

5.Run gel for checking K145205

6.Purify pLac+BRS+RFP+term and pSB1C3+RFP

 Nanodrop:
 pLac+RFP1      72.8ng/uL
 pLac+RFP2      22.5ng/uL
 pSB1C3+RFP1   105.4ng/uL
 pSB1C3+RFP2    91.5ng/uL
 pSB1C3+RFP3    65.3ng/uL

7.Run gel for pLac+RBS+YFP+term and pLac+RBS+CFP+term(PCR)

8.Digest pLac+BRS+RFP+term(XP)and pSB1C3+RFP(XP)

9.Extract pLac+BRS+RFP+term(XP)and pSB1C3+RFP(XP) and purify them

2010-10-11

1.Digest pLac+RBS+CFP+term(XP) and pLac+RBS+YFP+term(XP)

2.Ligate pLac+RFPlva

2010-10-12

1.3-in-1 for pLac+RFPlva

2.Run the gel for checking pLac+RFPlva

3.Run the Gel for pLac+RBS+YFP+Term and pLac+RBS+YFP+Term(PCR)(digestion(XP))

4.Run the gel for pLac+RFP(XP)and RFP+pSB1C3(XP)

5.Extract GFP, K145205 and pLac

6.Digest GFP(XP) and pLac(SP)

7.Purify pSB1A2(XP), pSB1C3(XP), pLac+RBS+RFP+term(XP), pLac+RBS+YFP+term(XP)and pLac+RBS+CFP+term(XP)

2010-10-14

1.Ligation for pLac+GFPlva, pLac+CFPlva, pLac+RFPlva, pLac+RBS+YFP+term with pSB1A2

2010-10-15

1.Colony PCR for pLac+RBS+YFP+term, pLac+RBS+CFP+term

2.Run gel for pLac+RBS+YFP+term, pLac+RBS+CFP+term

2010-10-21

1.Colony PCR for pLac+RBS+GFP+term, pLac+RBS+YFP+term, pLac+RBS+CFP+term

2.Run gel for pLac+RBS+GFP+term, pLac+RBS+YFP+term, pLac+RBS+CFP+term

NYMU-Taipei iGEM 2010 Team

@@ Line 26: / Line 26: @@
 |E0240||876bp||1114bp
 |-
-|E0240+lva||909bp||1147bp
+|E0240+LVA||909bp||1147bp
 |-
-|R0010+E0240+lva||1117bp||1355bp
+|R0010+E0240+LVA||1117bp||1355bp
 |}
@@ Line 51: / Line 51: @@
 |I13507||861bp||1099bp
 |-
-|I13507+lva||894bp||1132bp
+|I13507+LVA||894bp||1132bp
 |-
-|R0010+I13507+lva||1102bp||1340bp
+|R0010+I13507+LVA||1102bp||1340bp
 |}
@@ Line 59: / Line 59: @@
 '''Purpose'''
-After ligate CFPlva to Terminator and RBS , ligate to pLac.
+.After ligate CFPlva to Terminator and RBS , ligate to pLac.
+.Remove LVA from the sequences to construct the control.
 '''Material'''
@@ Line 89: / Line 91: @@
 '''Purpose'''
-After ligate YFPlva to Terminator and RBS , ligate to pLac.
+.After ligate YFPlva to Terminator and RBS , ligate to pLac.
+.Remove LVA from the sequences to construct the control.
 '''Material'''
@@ Line 165: / Line 169: @@
 .Run the gel.
-{{:Team:NYMU-Taipei/GEL|NYMU G0724 1.jpg|{{:Team:NYMU-Taipei/PCR|2m|15s|20s|90s|5m|rp=VR|fp=VF2}}|c=
-% agarose, 90V, 40min
+[[Image:0724.jpg]]
-{{:Team:NYMU-Taipei/GELC|=
-|1: Marker 1kb|-|-|n|=
-|2: positive|-|-|n|=
-|3: negative|-|-|n|=
-|4: CFPlva+Terminator|||n|=
-|5: CFPlva+Terminator|||n|=
-|6: CFPlva+Terminator|724|none|f|=
-|7: CFPlva+Terminator|758|none|f|=
-|8: YFPlva+Terminator|-|-|n|=
-|9: YFPlva+Terminator|-|-|n|=
-|10: RBS|-|-|n|=
-|11: Terminator|-|-|n|=
-|12: Marker 100bp|-|-|n|=
-}}positive control:GFP template}}
 .PCR to make the whole parts GFPlva and RFPlva.
 .Run the gel.
-{{:Team:NYMU-Taipei/GEL|NYMU G0724 2.jpg|{{:Team:NYMU-Taipei/PCR|2m|15s|20s|90s|5m|rp=VR|fp=VF2}}|c=
-% agarose, 90V, 40min
+[[Image:0724 2.jpg]]
-{{:Team:NYMU-Taipei/GELC|=
-|1: Marker 100bp|-|-|n|=
-|2: positive|-|-|n|=
-|3: GFPlva whole part|||m|=
-|4: RGPlva whole part|||m|=
-|5: negative|-|-|n|=
-|6: Marker 100bp|724|none|n|=
-}}positive control:GFP template}}
 .Digest GFPlva(XP) and RFPlva(XP).

SsrA Experiment

From 2010.igem.org

Latest revision as of 18:08, 27 October 2010

Contents

Our Goal

GFP

RFP

CFP

YFP

Our Experiment Data

2010-07-22

2010-07-23

2010-07-24

2010-07-26

2010-07-28

2010-07-29

2010-07-31

2010-08-02

2010-08-04

2010-08-05

2010-08-06

2010-08-07

2010-08-09

2010-08-10

2010-08-11

2010-08-12

2010-08-14

2010-08-17

2010-08-18

2010-08-19

2010-08-20

2010-08-21

2010-08-23

2010-08-24

2010-09-01

2010-09-02

2010-09-04

2010-09-11

2010-09-18

2010-09-30

2010-10-1

2010-10-4

2010-10-7

2010-10-9

2010-10-11

2010-10-12

2010-10-14

2010-10-15

2010-10-21