Berkeley LBL/JoyceCyano

From 2007.igem.org

< Berkeley LBL(Difference between revisions)
 
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'''Contruction of pET3a Derivatives Containing ''bchD'' and ''bchI'''''
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'''Contruction of pET3a Derivatives Containing ''chlD'' and ''chlI'''''
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1. Amplify Rhodobacter's gene and introduce restriction sites by [[Berkeley_LBL/PCRphusion|PCR (Using Phusion Polymerase)]], which allow cloning PCR fragments into pET3a
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1. Amplify ''Synecholystis Sp.'' gene and introduce restriction sites by [[Berkeley_LBL/PCRphusion|PCR (Using Phusion Polymerase)]], which allow cloning PCR fragments into pET3a
{| border =  
{| border =  
|-
|-
!
!
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!''bchD''  
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!''chlD''  
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!''bchI''
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!''chlI''
|-
|-
|length of gene fragment
|length of gene fragment
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|1695 b.p.
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|2031 b.p.
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|1005 b.p.
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|1074 b.p.
|-
|-
|Restriction sites introduced when amplified by PCR
|Restriction sites introduced when amplified by PCR
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|NdeI, BamHI
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|NdeI, BglI
|NdeI, BglI
|NdeI, BglI
|}
|}
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  Rhodobacter Genomic DNA     1 ul
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  ''Synecholystis Sp.'' Genomic DNA       1 ul
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  GC Buffer                   10 ul
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  HF Buffer                           10 ul
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  dNTP                         1 ul
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  dNTP                                 1 ul
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  Primer Mix                   5 ul
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  Primer Mix                           5 ul
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  Water                     27.5 ul
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  Water                             32.5 ul
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DMSO                      5.0 ul
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  Phusion Polymerase                 0.5 ul
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  Phusion Polymerase         0.5 ul
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  |  98 °C  
  |  98 °C  
  |  98 °C  
  |  98 °C  
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  |  52 °C  
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  |  62 °C  
  |  72 °C  
  |  72 °C  
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  |  8 sec
  |  8 sec
  |  30 sec
  |  30 sec
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  |  60 sec
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  |  70 sec
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  |  10 min
  |  10 min
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  |  98 °C  
  |  98 °C  
  |  98 °C  
  |  98 °C  
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  |  62 °C  
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  |  64 °C  
  |  72 °C  
  |  72 °C  
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  |  8 sec
  |  8 sec
  |  30 sec
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  |  32 sec
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  |  40 sec
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  |  10 min
  |  10 min
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{| border =  
{| border =  
|-
|-
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!''bchD''  
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!''chlD''  
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|NdeI, BamHI
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|NdeI, BglI
|-
|-
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!''bchI''
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!''chlI''
|NdeI, BglI
|NdeI, BglI
|}
|}
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4. Digested ''bchD'' and ''bchI'' are subjected to [[Berkeley_LBL/GelExtraction|Gel Extraction]] to ensure that only pure, digested DNA is obtained before doing ligation.
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4. Digested ''chlD'' and ''chlI'' are subjected to [[Berkeley_LBL/GelExtraction|Gel Extraction]] to ensure that only pure, digested DNA is obtained and before doing ligation.
5. Ligate digested and purified PCR fragments with digested pET3a by [[Berkeley_LBL/Ligation|Ligation]] yielding plasmids of pETBCHD and pETBCHI.
5. Ligate digested and purified PCR fragments with digested pET3a by [[Berkeley_LBL/Ligation|Ligation]] yielding plasmids of pETBCHD and pETBCHI.

Latest revision as of 02:55, 27 October 2007

Contruction of pET3a Derivatives Containing chlD and chlI

1. Amplify Synecholystis Sp. gene and introduce restriction sites by PCR (Using Phusion Polymerase), which allow cloning PCR fragments into pET3a

chlD chlI
length of gene fragment 2031 b.p. 1074 b.p.
Restriction sites introduced when amplified by PCR NdeI, BglI NdeI, BglI 
Synecholystis Sp. Genomic DNA        1 ul
HF Buffer                           10 ul
dNTP                                 1 ul
Primer Mix                           5 ul
Water                             32.5 ul
Phusion Polymerase                 0.5 ul


bchD
1.Initial Denaturation 2.Denaturation 3.Annealing 4.Extension 5.Repeat step 2 to 4 for 30 times 6.Final Extension
98 °C 98 °C 62 °C 72 °C 72 °C 4 °C
30 sec 8 sec 30 sec 70 sec 10 min forever


bchI
1.Initial Denaturation 2.Denaturation 3.Annealing 4.Extension 5.Repeat step 2 to 4 for 30 times 6.Final Extension
98 °C 98 °C 64 °C 72 °C 72 °C 4 °C
30 sec 8 sec 30 sec 40 sec 10 min forever

2. Do DNA Gel Electrophoresis to confirm that the length of the PCR fragments are the same as the corresponding target gene fragments.

3. Remove any leftover PCR enzyme in the samples by PCR Clean Up/Purification.

4. Digestion for PCR Products using specific restriction enzymes

chlD NdeI, BglI
chlI NdeI, BglI

4. Digested chlD and chlI are subjected to Gel Extraction to ensure that only pure, digested DNA is obtained and before doing ligation.

5. Ligate digested and purified PCR fragments with digested pET3a by Ligation yielding plasmids of pETBCHD and pETBCHI.

6. Use small portion of the plasmids to do Analytic Digestion.

7. Do KCM Competent Cell Transformation to subclone plasmids into DH10B competent cells, which have been done by KCM Competent Cell Production.

8. Pick colonies and innoculate in 2ml LB + 2ul Carbencilin in 37°C shaker overnight.

9. Extract plasmid DNA from bacteria by [[Berkeley_LBL/Miniprep|Miniprep].

10. Confirm that the plasmid DNA contains the right construct by Digestion for Miniprepped DNA and Analytic Digestion.

11. Do KCM Competent Cell Transformation to subclone plasmids into BL21, which have been done by KCM Competent Cell Production.


Protein Expression

Protein Analysis

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