Haynes Lab:Notebook/Engineering PC-TFs/2013/02/14

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==Summary==
==Summary==
-
*  
+
* * '''Performed BsmBI/ T4 ligase mediated assembly'''
 +
* BsmBI cuts the DNA fragments and creates complementary overhangs.
 +
* Complementary sticky ends anneal via base pairing.
 +
* T4 ligase seals gaps in the phosphodiester DNA backbone.
 +
{| {{table}}
 +
| bgcolor="grey" | Reagent
 +
| bgcolor="grey" | Vol.
 +
| rowspan=7 | '''Thermal cycling'''
 +
* [45°C, 2 min.; 16°C 5 min.] x25
 +
* 60°C, 10 min.
 +
* 80°C, 20 min.
 +
* 4°C, ∞
 +
|-
 +
| 20 fmol (1 μL) of each DNA part || up to 8.0
 +
|-
 +
| 10x T4 ligase buffer (Promega) || 1.0
 +
|-
 +
| T4 ligase (NEB) || 0.25
 +
|-
 +
| BsmBI || 0.5
 +
|-
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| dH<sub>2</sub>O || 0.25
 +
|-
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| &nbsp; || 10.0 μL
 +
|}
 +
{| {{table}} border="1" cellspacing="3" <!-- Golden Gate Rxn. table -->
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|- valign="top"
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| bgcolor="grey" | Reagent
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| bgcolor="grey" | 1
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| bgcolor="grey" | 2
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| bgcolor="grey" | 3
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|-
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| gg2 pSB1A3 || 1.0 || 1.0 || 1.0
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|-
 +
| gg3 hPCD || 1.0 || 1.0 || 1.0
 +
|-
 +
| BL02 || 1.0 || --- || ---
 +
|-
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| BL03 || --- || 1.0 || ---
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|-
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| BL04 || --- || --- || 1.0
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|-
 +
| 10x ligase buffer || 1.0 || 1.0 || 1.0
 +
|-
 +
| NEB T4 lgase || 0.25 || 0.25 || 1.0
 +
|-
 +
| BsmBI || 0.5 || 0.5 || 0.5
 +
|-
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| dH<sub>2</sub>O || 5.25 || 5.25 || 5.25
 +
|-
 +
| Total|| 10.0 || 10.0
 +
|}
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<font size=3>'''Bacterial transformation'''</font>
 +
* Added total volume (10.0 μL) to 50 μL chemically competent cells  (e.g., BL21) in a 2.0 mL tube.
 +
* Incubated on ice for 2 min., heat shock at 42°C for exactly 45 sec., and placed on ice.
 +
* Added 800 μL sterile SOC medium.
 +
* Grow with shaking at 37°C for 30 min.(''Taped tubes to the shaker rack.'') 
 +
* Pelleted the cells at top speed in a microcentrifuge for 3 min. at room temperature.
 +
* Discarded the supernatant. Resuspended the cells in 100 μL LB + antibiotic.
 +
* Plate cells on pre-warmed LB agar + antibiotic. (''I plated 100 μL of the cells. Then put beads on plates and shook.) Protocol didn't specify.'')  Grow overnight at 37°C.
 +
* Check results tomorrow.
 +
 +
There were no colonies on the plates. It's possible that the concentration of the ligation product is to low, so I will try to amplify.
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Revision as of 01:23, 16 February 2013

Engineering PC-TFs Main project page
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Summary

  • * Performed BsmBI/ T4 ligase mediated assembly
  • BsmBI cuts the DNA fragments and creates complementary overhangs.
  • Complementary sticky ends anneal via base pairing.
  • T4 ligase seals gaps in the phosphodiester DNA backbone.
Reagent Vol. Thermal cycling
  • [45°C, 2 min.; 16°C 5 min.] x25
  • 60°C, 10 min.
  • 80°C, 20 min.
  • 4°C, ∞
20 fmol (1 μL) of each DNA part up to 8.0
10x T4 ligase buffer (Promega) 1.0
T4 ligase (NEB) 0.25
BsmBI 0.5
dH2O 0.25
  10.0 μL
Reagent 1 2 3
gg2 pSB1A3 1.0 1.0 1.0
gg3 hPCD 1.0 1.0 1.0
BL02 1.0 --- ---
BL03 --- 1.0 ---
BL04 --- --- 1.0
10x ligase buffer 1.0 1.0 1.0
NEB T4 lgase 0.25 0.25 1.0
BsmBI 0.5 0.5 0.5
dH2O 5.25 5.25 5.25
Total 10.0 10.0

Bacterial transformation

  • Added total volume (10.0 μL) to 50 μL chemically competent cells (e.g., BL21) in a 2.0 mL tube.
  • Incubated on ice for 2 min., heat shock at 42°C for exactly 45 sec., and placed on ice.
  • Added 800 μL sterile SOC medium.
  • Grow with shaking at 37°C for 30 min.(Taped tubes to the shaker rack.)
  • Pelleted the cells at top speed in a microcentrifuge for 3 min. at room temperature.
  • Discarded the supernatant. Resuspended the cells in 100 μL LB + antibiotic.
  • Plate cells on pre-warmed LB agar + antibiotic. (I plated 100 μL of the cells. Then put beads on plates and shook.) Protocol didn't specify.) Grow overnight at 37°C.
  • Check results tomorrow.

There were no colonies on the plates. It's possible that the concentration of the ligation product is to low, so I will try to amplify.


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