User:Karmella Haynes/Notebook/BioBrick cloning/2013/01/17

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==mm/dd/yy==
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==01/17/13==
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* Minipreps: check Golden Gate assembly clones (trial 3)
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'''Minipreps'''<br>
'''Minipreps'''<br>
* Check with E/P digests
* Check with E/P digests
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* Minipreps from colonies on Plate #2 (Promega home-made ligation buffer trial)
{| {{table}} border="1" cellspacing="3" <!-- Digest check rxn. table -->
{| {{table}} border="1" cellspacing="3" <!-- Digest check rxn. table -->
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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. BB 1 = size<br>2. BB2 = size<br>
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| rowspan="7" | <u>Expected:</u><br>1. Plate 2-1 = 2000 (v), 2706 (i)<br>2. Plate 2-2 = 2000 (v), 2706 (i)<br>3. Plate 2-3 (red) = 2000 (v), 2706 (i)<br><br>4. Plate 2-4 = 2000 (v), 2706 (i)<br>5. pSB1A3+RFP = 2000 (v), ~1200 (i)<br>6. hPCD/V0120 = 3200 (v), 186 (i)<br>7. BL01 = 3200 (v), 2520 (i)<br>
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| rowspan="7" | <!-- [[Image:GelImage.jpg|400px|Hover name]]<br>15 μL/lane; 1% agarose; [http://openwetware.org/wiki/Image:KAH_Fermentas_GeneRuler_1kbplus.jpg Ladder] -->
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| rowspan="7" | [[Image:KAH011813_gel1.jpg|300px|E/P digests]]<br>15 μL/lane; 1% agarose; [http://openwetware.org/wiki/Image:KAH_Fermentas_GeneRuler_1kbplus.jpg Ladder]
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| DNA(plasmid) || 2.0 μL
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| DNA(plasmid) || 3.0 μL
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| 10X buffer || 1.5
| 10X buffer || 1.5

Revision as of 17:16, 18 January 2013

Karmella's BioBrick Cloning Main project page
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01/17/13

  • Minipreps: check Golden Gate assembly clones (trial 3)


Minipreps

  • Check with E/P digests
  • Minipreps from colonies on Plate #2 (Promega home-made ligation buffer trial)
Reagent Volume Expected:
1. Plate 2-1 = 2000 (v), 2706 (i)
2. Plate 2-2 = 2000 (v), 2706 (i)
3. Plate 2-3 (red) = 2000 (v), 2706 (i)

4. Plate 2-4 = 2000 (v), 2706 (i)
5. pSB1A3+RFP = 2000 (v), ~1200 (i)
6. hPCD/V0120 = 3200 (v), 186 (i)
7. BL01 = 3200 (v), 2520 (i)
 E/P digests
15 μL/lane; 1% agarose; Ladder
DNA(plasmid) 3.0 μL
10X buffer 1.5
EcoRI 1.0
PstI 1.0
dH2O 9.5
  15 μL --> 37°C/ ~15 min.

Assemblies

  1. BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size
  2. BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size


  • Digests (Fermentas FD)
    • Specific notes
Reagent Volume
DNA (plasmid) up to 25 μL
10x buffer 3.0
enzyme 1 1.0
enzyme 2 1.0
dH2O ---
  30 μL --> 37°C/ ~30 min.


  • Measure conc.'s
Sample OD260 260/280 ng/μL
1. Digested part (a/b) --- --- ---
2. Digested part (c/d) --- --- ---


  • Dephosphorylation (Roche)
Reagent Volume
DNA (clean digest) up to 17 μL (500 ng)
10x buffer d.p. 2.0
phosphatase 1.0
dH2O ---
  20 μL --> 37°C/ 10 min.; 75°C/ 2 min.; [final] = 25 ng/μL


  • Ligations
Ligation Plate results (lig : neg crtl) mm/dd/yy
1. insert(a/b)/size, ## ng + vector(c/d)/size, ## ng new BioBrick #:1 (Pick #)
2. vector(c/d)/ ## ng  
  1 2
Insert DNA ### ---
Vector DNA ### ###
2x lgn buf (Roche) ### ###
T4 ligase (NEB) 1.0 1.0
dH2O ### ###
  # μL # μL

Oligo annealing

  1. New BB 1
  2. New BB 2
DNA (oligos, 100 μM) up to 18 μL (3 μL ea.)
10x annealing buffer 2.0
dH2O ---
  20 μL --> 100°C (water bath)/ 5 min.; Cool to R.T. overnight



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