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Team:Todai-Tokyo/Notebook/LDLR
From 2009.igem.org
(→September) |
(changed "zenaku" characters to "hankaku") |
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*Mix 1ul of DNA with 100ul of competent cells on ice. | *Mix 1ul of DNA with 100ul of competent cells on ice. | ||
*Leave on ice for 30 minutes. | *Leave on ice for 30 minutes. | ||
| - | *Heat shock at | + | *Heat shock at 42ºC for 45 seconds. |
*Leave on ice for 2 minutes. | *Leave on ice for 2 minutes. | ||
| - | *Add 500ul of LB and incubate at | + | *Add 500ul of LB and incubate at 37ºC for 1 hour. |
*Plate on LB-ampicillin plates. | *Plate on LB-ampicillin plates. | ||
| Line 49: | Line 49: | ||
0.5ul Pfu Ultra<BR> | 0.5ul Pfu Ultra<BR> | ||
15.05ul MilliQ water<BR> | 15.05ul MilliQ water<BR> | ||
| - | + | ￬<BR> | |
Performed PCR using the following program:<BR> | Performed PCR using the following program:<BR> | ||
| - | 1. | + | 1. 95ºC 2min<BR> |
| - | 2. | + | 2. 95ºC 30sec <BR> |
| - | 3. | + | 3. 55ºC 30sec<BR> |
| - | 4. 72. | + | 4. 72.5ºC 60sec<BR> |
5. repeat 2-4 29times<BR> | 5. repeat 2-4 29times<BR> | ||
| - | 6. | + | 6. 25ºC forever<BR> |
<BR> | <BR> | ||
PCR successful<BR> | PCR successful<BR> | ||
| Line 67: | Line 67: | ||
2ul 5×infusion reaction buffer<BR> | 2ul 5×infusion reaction buffer<BR> | ||
1ul infusion enzyme<BR> | 1ul infusion enzyme<BR> | ||
| - | + | ￬<BR> | |
| - | + | 37ºC 15min<BR> | |
| - | + | 50ºC 15min<BR> | |
| - | + | ￬<BR> | |
TE buffer up to 20ul<BR> | TE buffer up to 20ul<BR> | ||
| - | + | ￬<BR> | |
added 10ul of the sample to DH5α (090614) and put on ice for 15 min.<BR> | added 10ul of the sample to DH5α (090614) and put on ice for 15 min.<BR> | ||
| - | + | ￬<BR> | |
| - | + | 42ºC 45sec<BR> | |
| - | + | ￬<BR> | |
added 500ul LB broth to the tube.<BR> | added 500ul LB broth to the tube.<BR> | ||
| - | + | ￬<BR> | |
placed it on LB ampicilin plate. <BR> | placed it on LB ampicilin plate. <BR> | ||
<BR> | <BR> | ||
| Line 87: | Line 87: | ||
<BR> | <BR> | ||
put a small amount of single colony into each tube with 5ul MilliQ water<BR> | put a small amount of single colony into each tube with 5ul MilliQ water<BR> | ||
| - | + | ￬<BR> | |
| - | + | 95ºC 5min<BR> | |
| - | + | ￬<BR> | |
PCR reaction<BR> | PCR reaction<BR> | ||
1ul 10×buffer <BR> | 1ul 10×buffer <BR> | ||
| Line 97: | Line 97: | ||
0.1ul 3’-primer<BR> | 0.1ul 3’-primer<BR> | ||
2.92ul MilliQ water<BR> | 2.92ul MilliQ water<BR> | ||
| - | + | ￬<BR> | |
added the PCR reaction to each tube.<BR> | added the PCR reaction to each tube.<BR> | ||
| - | + | ￬<BR> | |
Performed PCR using the following program:<BR> | Performed PCR using the following program:<BR> | ||
| - | 1. | + | 1. 95ºC 2min<BR> |
| - | 2. | + | 2. 95ºC 30sec <BR> |
| - | 3. | + | 3. 55ºC 30sec<BR> |
| - | 4. 72. | + | 4. 72.5ºC 120sec<BR> |
| - | 5. repeat 2-4 | + | 5. repeat 2-4 29 times<BR> |
| - | 6. | + | 6. 25ºC forever<BR> |
<BR> | <BR> | ||
PCR unsuccessful・・・.<BR> | PCR unsuccessful・・・.<BR> | ||
| Line 119: | Line 119: | ||
1ul plasmid(0.15ug/ul)<BR> | 1ul plasmid(0.15ug/ul)<BR> | ||
0.5ul 5'or3'primer(3.2pmol/ul)<BR> | 0.5ul 5'or3'primer(3.2pmol/ul)<BR> | ||
| - | + | ￬<BR> | |
PCR Program<BR> | PCR Program<BR> | ||
| - | 1. | + | 1.96ºC 2min<BR> |
| - | 2. | + | 2.96ºC 10sec<BR> |
| - | 3. | + | 3.55ºC 5sec<BR> |
| - | 4. | + | 4.60ºC 3min <BR> |
5.go to 2.29times<BR> | 5.go to 2.29times<BR> | ||
| - | 6. | + | 6.25ºC forever<BR> |
| - | + | ￬<BR> | |
add 0.5ul PHOSPHATASE ALKALINE shrimp<BR> | add 0.5ul PHOSPHATASE ALKALINE shrimp<BR> | ||
| - | + | ￬<BR> | |
| - | + | 37ºC 1hr incubate<BR> | |
| - | + | ￬<BR> | |
add 1ul 3MNaOAc<BR> | add 1ul 3MNaOAc<BR> | ||
| - | + | ￬<BR> | |
add 25ul EtOH<BR> | add 25ul EtOH<BR> | ||
| - | + | ￬<BR> | |
| - | 20000xg | + | 20000xg 4ºC 10min centrifugation<BR> |
| - | + | ￬<BR> | |
put off supernatant<BR> | put off supernatant<BR> | ||
| - | + | ￬<BR> | |
dry tubes<BR> | dry tubes<BR> | ||
| - | + | ￬<BR> | |
add 15ul HiDi<BR> | add 15ul HiDi<BR> | ||
| - | + | ￬<BR> | |
put them in the sequence machine<BR> | put them in the sequence machine<BR> | ||
| Line 149: | Line 149: | ||
colony PCR again, using 7/20 protocol.<BR> | colony PCR again, using 7/20 protocol.<BR> | ||
PCR program<BR> | PCR program<BR> | ||
| - | 1. | + | 1.95ºC 2min <BR> |
| - | 2. | + | 2.95ºC 30sec<BR> |
| - | 3. | + | 3.55ºC 30sec<BR> |
| - | 4.72. | + | 4.72.5ºC 150sec<BR> |
5.go to 2. 29times<BR> | 5.go to 2. 29times<BR> | ||
| Line 163: | Line 163: | ||
PCR of GFP for fusion<BR> | PCR of GFP for fusion<BR> | ||
program<BR> | program<BR> | ||
| - | 1. | + | 1.95ºC 2min<BR> |
| - | 2. | + | 2.95ºC 30sec<BR> |
| - | 3. | + | 3.55ºC 30sec<BR> |
| - | 4.72. | + | 4.72.5ºC 20sec<BR> |
5.go to 2. 29 times<BR> | 5.go to 2. 29 times<BR> | ||
| - | 6. | + | 6.25ºC forever<BR> |
<BR> | <BR> | ||
We found that the length of these PCR product till now was longer than that of LDLR.<BR> | We found that the length of these PCR product till now was longer than that of LDLR.<BR> | ||
| Line 178: | Line 178: | ||
*look for the best PCR program<BR> | *look for the best PCR program<BR> | ||
→DMSO 5% or 10%<BR> | →DMSO 5% or 10%<BR> | ||
| - | →annealing temparature | + | →annealing temparature 55ºC or 60ºC<BR><BR> |
result<BR> | result<BR> | ||
the best program<BR> | the best program<BR> | ||
10% DMSO<BR> | 10% DMSO<BR> | ||
| - | 1. | + | 1.95ºC 2min<BR> |
| - | 2. | + | 2.95ºC 30sec<BR> |
| - | 3. | + | 3.60ºC 30sec<BR> |
| - | 4.72. | + | 4.72.5ºC 1min<BR> |
5.go to 2. 29 times<BR> | 5.go to 2. 29 times<BR> | ||
| - | 6. | + | 6.25ºC forever<BR> |
purify the PCR product using Promega kit and insert it in iGEM part(plate1-7D:Gal1 promoter) <BR> | purify the PCR product using Promega kit and insert it in iGEM part(plate1-7D:Gal1 promoter) <BR> | ||
And, insert it and GFP in iGEM part(plate1-7D:Gal1 promoter) | And, insert it and GFP in iGEM part(plate1-7D:Gal1 promoter) | ||
Revision as of 16:28, 18 October 2009
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Contents |
Plan
Aim: Create yeast cells that express LDLR on their cell membrane
Methods:
- Clone the LDLR gene.
- Create biobrick of LDLR.
7/6
Overview:
1.PCR LDLR gene from plasmid containing LDLR cDNA
2.gel-purify DNA from the PCR product
3.insert the DNA to vector (iGEM parts)
4.transform into E. coli and select for ampicillin resistance
5.check for transformation success using colony PCR by LDLR primers
Constructs to be created:
pGal1-Kozak-LDLR-terminator
Obtaining DNA:
Resuspended DNA in the following wells with 10ul water:
plate 1 7D
pGal1(including Kozak sequence)
[http://partsregistry.org/wiki/index.php?title=Part:BBa_J63006 Gal1 promoter]
Transformed 1ul of each of the above into DH5a competent cells:
Transformation
- Mix 1ul of DNA with 100ul of competent cells on ice.
- Leave on ice for 30 minutes.
- Heat shock at 42ºC for 45 seconds.
- Leave on ice for 2 minutes.
- Add 500ul of LB and incubate at 37ºC for 1 hour.
- Plate on LB-ampicillin plates.
7/7
Miniprep of E.coli cells containing LDLR gene with Promega, Wizard Plus SV Miniprep DNA Purification System
Successful
7/19
PCR of LDLR
0.4ul 50uM 5’primer
0.4ul 50uM 3’primer
1.6ul 2.5mM dNTP
2ul 10×Pfu Ultra 2 buffer
0.05ul LDLR plasmid
0.5ul Pfu Ultra
15.05ul MilliQ water
￬
Performed PCR using the following program:
1. 95ºC 2min
2. 95ºC 30sec
3. 55ºC 30sec
4. 72.5ºC 60sec
5. repeat 2-4 29times
6. 25ºC forever
PCR successful
We cut the region of LDLR out of the gel and purified PCR product using Promega kit.
infusion of LDLR
4ul PCR product (12.35ug/ml)
3ul vector (iGEM parts plate1 D-3, 14.95ug/ml)
2ul 5×infusion reaction buffer
1ul infusion enzyme
￬
37ºC 15min
50ºC 15min
￬
TE buffer up to 20ul
￬
added 10ul of the sample to DH5α (090614) and put on ice for 15 min.
￬
42ºC 45sec
￬
added 500ul LB broth to the tube.
￬
placed it on LB ampicilin plate.
7/20
colony PCR
put a small amount of single colony into each tube with 5ul MilliQ water
￬
95ºC 5min
￬
PCR reaction
1ul 10×buffer
0.8ul 2.5mMdNTP
0.08ul Ex-Taq
0.1ul 5’-primer
0.1ul 3’-primer
2.92ul MilliQ water
￬
added the PCR reaction to each tube.
￬
Performed PCR using the following program:
1. 95ºC 2min
2. 95ºC 30sec
3. 55ºC 30sec
4. 72.5ºC 120sec
5. repeat 2-4 29 times
6. 25ºC forever
PCR unsuccessful・・・.
7/25
gal1 sequencing by BIG DYE
1.8ul 5xB.D.3.1.buffer
0.4ul B.D.3.1.
6.3ul MilliQ water
1ul plasmid(0.15ug/ul)
0.5ul 5'or3'primer(3.2pmol/ul)
￬
PCR Program
1.96ºC 2min
2.96ºC 10sec
3.55ºC 5sec
4.60ºC 3min
5.go to 2.29times
6.25ºC forever
￬
add 0.5ul PHOSPHATASE ALKALINE shrimp
￬
37ºC 1hr incubate
￬
add 1ul 3MNaOAc
￬
add 25ul EtOH
￬
20000xg 4ºC 10min centrifugation
￬
put off supernatant
￬
dry tubes
￬
add 15ul HiDi
￬
put them in the sequence machine
7/26
colony PCR again, using 7/20 protocol.
PCR program
1.95ºC 2min
2.95ºC 30sec
3.55ºC 30sec
4.72.5ºC 150sec
5.go to 2. 29times
but,unsucessful.
7/27
Miniprep of E.coli cells containing LDLR gene(that yesterday picked up and cultured) with Promega, Wizard Plus SV Miniprep DNA Purification System
using AGE, found a colony that has LDLR infusion plasmid
August
PCR of GFP for fusion
program
1.95ºC 2min
2.95ºC 30sec
3.55ºC 30sec
4.72.5ºC 20sec
5.go to 2. 29 times
6.25ºC forever
We found that the length of these PCR product till now was longer than that of LDLR.
- read the sequence of LDLR cDNA→the result didn't conform with NCBI datebase
- change PCR program→didn't get the PCR product whose length was correct
September
We got new LDLR cDNA!
- look for the best PCR program
→DMSO 5% or 10%
→annealing temparature 55ºC or 60ºC
result
the best program
10% DMSO
1.95ºC 2min
2.95ºC 30sec
3.60ºC 30sec
4.72.5ºC 1min
5.go to 2. 29 times
6.25ºC forever
purify the PCR product using Promega kit and insert it in iGEM part(plate1-7D:Gal1 promoter)
And, insert it and GFP in iGEM part(plate1-7D:Gal1 promoter)
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