User:Karmella Haynes/Notebook/BioBrick cloning/2013/01/05

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| bgcolor=#cfcfcf | Reagent
| bgcolor=#cfcfcf | Reagent
| bgcolor=#cfcfcf | Volume  
| bgcolor=#cfcfcf | Volume  
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| rowspan="7" | <u>Expected:</u><br>1. V0120 = 3200<br>2. pSB1A3 = 2000<br>3. hPCD = 186<br>4. BL01 = 2520
+
| rowspan="7" | <u>Expected:</u><br>G1. V0120 = 3200<br>G2. pSB1A3 = 2000<br>G3. hPCD = 186<br>G4. BL01 = 2520
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| rowspan="7" | [[Image:GelImage.jpg|400px|Hover name]]<br>10 μL/lane; 1% agarose; [http://openwetware.org/wiki/Image:KAH_Fermentas_GeneRuler_1kbplus.jpg Ladder]
+
| rowspan="7" | [[Image:KAH010513_gel1.jpg|300px|Hover name]]<br>10 μL/lane; 1% agarose; [http://openwetware.org/wiki/Image:KAH_Fermentas_GeneRuler_1kbplus.jpg Ladder]
|-
|-
| DNA(plasmid) || 0.5 μL
| DNA(plasmid) || 0.5 μL
Line 128: Line 128:
| bgcolor=#cfcfcf | Reagent
| bgcolor=#cfcfcf | Reagent
| bgcolor=#cfcfcf | Volume  
| bgcolor=#cfcfcf | Volume  
-
| rowspan="7" | <u>Expected:</u><br>1. V0120 = 3200<br>2. pSB1A3 = 2000<br>3. hPCD = 186<br>4. BL01 = 2520
+
| rowspan="7" | <u>Expected:</u><br>gg1. V0120 = 3200<br>gg2. pSB1A3 = 2000<br>gg3. hPCD = 186<br>gg4. BL01 = 2520
-
| rowspan="7" | [[Image:GelImage.jpg|400px|Hover name]]<br>10 μL/lane; 1% agarose; [http://openwetware.org/wiki/Image:KAH_Fermentas_GeneRuler_1kbplus.jpg Ladder]
+
| rowspan="7" | [[Image:KAH010513_gel1.jpg|300px|Hover name]]<br>10 μL/lane; 1% agarose; [http://openwetware.org/wiki/Image:KAH_Fermentas_GeneRuler_1kbplus.jpg Ladder]
|-
|-
| DNA(plasmid) || 0.5 μL
| DNA(plasmid) || 0.5 μL

Revision as of 20:32, 5 January 2013

Karmella's BioBrick Cloning Main project page
Previous entry      Next entry

01/05/13

  • Golden gate: PCR parts, complete protocol for Brady's construct
  • Gibson: PCR parts; waiting on BsmBI from NEB


Gibson Assembly

  1. hPCD + BL01 + V0120
  2. hPCD + BL01 + pSB1A3


PCR

  1. V0120, Gib_BBS F (Gib0001) / Gib_BBP R (Gib0002)
  2. pSB1A3, Gib_BBS F (Gib0001) / Gib_BBP R (Gib0002)
  3. hPCD, BBP-hPCD fwd (BL9) / hPCD-BL01 rev (BL7)
  4. BL01, hPCD-BL01 fwd (BL8) / BL01-BBS rev (BL10)
Reagent Volume Expected:
G1. V0120 = 3200
G2. pSB1A3 = 2000
G3. hPCD = 186
G4. BL01 = 2520 		Hover name
10 μL/lane; 1% agarose; Ladder
DNA(plasmid) 0.5 μL
10 μM primer 1 1.0
10 μM primer 2 1.0
2x GoTaq mix 25.0
dH2O 22.5
  50 μL
  • 95°C, 3 min.
  • [95°C, 30 sec.; 57°C, 30 sec.; 72°C, 2 min.] x 30
  • 72°C, 3 min.
  • 4°C, ∞

Measure DNA Concentrations

Sample OD 260 260/ 280 ng/μL
G1 V0120 0.108 1.801 108.375
G2 pSB1A3 0.101 1.849 100.553
G3 hPCD 0.034 1.876 33.586
G4 BL01 0.113 1.828 112.79


Reaction set-up

  • Use 0.2 - 0.5 pmol, per NEB's suggestion
  • pmols = ng x 1000 / bp x 650 daltons; ng = (pmols x bp x 650 daltons) / 1000
  • Total volume of DNA = 5.0 μL max

1. hPCD + BL01 + V0120

  • vector V0120, 0.1 pmol = 208 ng = 1.9 μL (use 1.4 μL)
  • 2:1 insert hPCD, 0.2 pmol = 24 ng = 0.7 μL
  • 2:1 insert BL01, 0.2 pmol = 328 ng = 2.9 μL

2. hPCD + BL01 + V0120

  • vector pSB1A3, 0.1 pmol = 130 ng = 1.3 μL
  • 2:1 insert hPCD, 0.2 pmol = 24 ng = 0.7 μL (use 0.8 μL)
  • 2:1 insert BL01, 0.2 pmol = 328 ng = 2.9 μL


Gibson reactions:

  1. hPCD + BL01 + V0120
  2. V0120
  3. hPCD + BL01 + pSB1A3
  4. pSB1A3
Reagent 1 2 3 4
Vector 1.4 1.4 1.3 1.3
Ins 1 0.7 --- 0.8 ---
Ins 2 2.9 --- 2.9 ---
dH2O --- 3.6 --- 3.7
  5.0 μL
  • Add each to one aliquot of 15.0 Gibson mix (Rene); total = 20.0 μL
  • Thermal cycler: 50°C,60 min.; 4°C, ∞
  • Transform


Golden Gate Assembly

  • Try new protocol from Dave Savage
  1. hPCD + BL01 + V0120
  2. hPCD + BL01 + pSB1A3
  • Check the sequences for BsmBI sites!

PCR

  1. V0120, gg_BBS F (gg0001) / gg_BBP R (gg0002)
  2. pSB1A3, gg_BBS F (gg0001) / gg_BBP R (gg0002)
  3. hPCD, gg_BBP-hPCD F (gg0003) / gg_hPCD-BL01 R (gg0004)
  4. BL01, gg_BL01 F (gg0004) / gg_BL01-BBS R (gg0005)
Reagent Volume Expected:
gg1. V0120 = 3200
gg2. pSB1A3 = 2000
gg3. hPCD = 186
gg4. BL01 = 2520 		Hover name
10 μL/lane; 1% agarose; Ladder
DNA(plasmid) 0.5 μL
10 μM primer 1 1.0
10 μM primer 2 1.0
2x GoTaq mix 25.0
dH2O 22.5
  50 μL
  • 95°C, 3 min.
  • [95°C, 30 sec.; 57°C, 30 sec.; 72°C, 2 min.] x 30
  • 72°C, 3 min.
  • 4°C, ∞


Measure DNA Concentrations

Sample OD 260 260/ 280 ng/μL
gg1 V0120 0.099 1.834 98.549
gg2 pSB1A3 0.068 1.758 67.725
gg3 hPCD 0.022 1.72 22.485
gg4 BL01 0.056 1.707 55.883




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