User:Karmella Haynes/Notebook/BioBrick cloning/2013/01/07

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(Autocreate 2013/01/07 Entry for User:Karmella_Haynes/Notebook/BioBrick_cloning)
Current revision (21:36, 7 January 2013) (view source)
(01/07/13)
 
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==mm/dd/yy==
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==01/07/13==
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* Line item 1
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* Gibson re-transformation: grow cultures
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* Line item 2
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* Re-transformation: 1x Gibson for pSB1A3 vector assemblies (3 & 4)
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----
----
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'''Minipreps'''<br>
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'''Gibson Re-transformation Results (1/06/13)'''<br>
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* Check with E/P digests
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* Number of colonies did not improve. Only 1 colony on hPCD + BL01 + V0120 plate
 +
* Streaks from yesterday: streak from plate 3 (hPCD + BL01 + pSB1A3 1xGibson) showed no color, whereas streak from plate 7 (hPCD + BL01 + pSB1A3 1/4x Gibson), showed RFP expression. The pSB1A3 template carries RFP.
 +
* Grow 2x 2 mL cultures from plate 3 streak to investigate whether an insert replaced RFP.
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{| {{table}} border="1" cellspacing="3" <!-- Digest check rxn. table -->
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* Do Zymo minipreps
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|- valign="top"
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| bgcolor=#cfcfcf | Reagent
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| 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" | <!-- [[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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|-
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| DNA(plasmid) || 2.0 μL
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|-
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| 10X buffer || 1.5
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|-
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| EcoRI || 1.0
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|-
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| PstI || 1.0
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|-
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| dH<sub>2</sub>O || 9.5
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|-
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| &nbsp; || 15 μL --> 37°C/ ~15 min.
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|}
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----
----
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'''Assemblies'''
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'''Gibson Re-transformation'''<br>
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# BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size
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# hPCD + BL01 + pSB1A3 (#3), 1xGibson, '''6.0 μL'''
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# BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size
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# pSB1A3 (#4), 1xGibson, '''6.0 μL'''
 +
* Add to 50 μL cells; ice/ 10 min.
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* Plate on 100 μg/mL amp LB agar
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* Digests (Fermentas FD)
 
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** Specific notes
 
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{| {{table}} cellspacing="3" <!-- Digest rxn. table -->
 
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|- valign="top"
 
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| bgcolor=#cfcfcf | Reagent
 
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| bgcolor=#cfcfcf | Volume
 
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| rowspan="7" | <!-- [[Image:GelImage.jpg|270px|Hover name]]<br>30 μL/lane, 1% agarose; [http://openwetware.org/wiki/Image:KAH_Fermentas_GeneRuler_1kbplus.jpg Ladder] -->
 
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|-
 
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| DNA (plasmid) || up to 25 μL
 
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|-
 
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| 10x buffer || 3.0
 
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|-
 
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| enzyme 1 || 1.0
 
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|-
 
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| enzyme 2 || 1.0
 
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|-
 
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| dH<sub>2</sub>O || ---
 
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|-
 
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| &nbsp; || 30 μL --> 37°C/ ~30 min.
 
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|}
 
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* Measure conc.'s
 
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{| {{table}} cellspacing="3" <!-- [DNA] table -->
 
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|- bgcolor=#cfcfcf
 
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| Sample || OD260 || 260/280 || ng/μL
 
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|-
 
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| 1. Digested part (a/b) || --- || --- || ---
 
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|-
 
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| 2. Digested part (c/d) || --- || --- || ---
 
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|}
 
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* Dephosphorylation (Roche)
 
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{| {{table}} cellspacing="3" <!-- Dephos table -->
 
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|-
 
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| bgcolor=#cfcfcf | Reagent
 
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| bgcolor=#cfcfcf | Volume
 
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|-
 
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| DNA (clean digest) || up to 17 μL (500 ng)
 
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|-
 
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| 10x buffer d.p. || 2.0
 
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|-
 
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| phosphatase || 1.0
 
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|-
 
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| dH<sub>2</sub>O || ---
 
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|-
 
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| &nbsp; || 20 μL --> 37°C/ 10 min.; 75°C/ 2 min.; [final] = 25 ng/μL
 
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|}
 
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* Ligations
 
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{| {{table}} cellspacing="3" <!-- Ligations table -->
 
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|- bgcolor=#cfcfcf
 
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| Ligation || <font color="blue"><u>Plate results (lig : neg crtl)</u> mm/dd/yy</font>
 
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|-
 
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| 1. insert(a/b)/size, ## ng + vector(c/d)/size, ## ng || <font color="blue">new BioBrick #:1 (Pick #)</font>
 
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|-
 
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| 2. vector(c/d)/ ## ng || &nbsp;
 
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|}
 
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{| {{table}} cellspacing="3" <!-- Ligation rxn table -->
 
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| &nbsp;            || 1    || 2    ||
 
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|-
 
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| Insert DNA        || ###  || ---  ||
 
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|-
 
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| Vector DNA        || ###  || ###  ||
 
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|-
 
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| 2x lgn buf (Roche) || ###  || ###  ||
 
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|-
 
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| T4 ligase (NEB)    || 1.0  || 1.0  ||
 
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|-
 
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| dH<sub>2</sub>O    || ###  || ###  ||
 
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|-
 
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| &nbsp;            || # μL || # μL ||
 
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|}
 
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----
 
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'''Oligo annealing'''
 
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# New BB 1
 
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# New BB 2
 
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{| class="wikitable" border="0" cellspacing="3" <!-- Oligo annealing rxn table -->
 
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| DNA (oligos, 100 μM) || up to 18 μL (3 μL ea.)
 
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|-
 
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| 10x annealing buffer || 2.0
 
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|-
 
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| dH<sub>2</sub>O || ---
 
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|-
 
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| &nbsp; || 20 μL --> 100°C (water bath)/ 5 min.; Cool to R.T. overnight
 
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|}
 

Current revision

Karmella's BioBrick Cloning Main project page
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01/07/13

  • Gibson re-transformation: grow cultures
  • Re-transformation: 1x Gibson for pSB1A3 vector assemblies (3 & 4)



Gibson Re-transformation Results (1/06/13)

  • Number of colonies did not improve. Only 1 colony on hPCD + BL01 + V0120 plate
  • Streaks from yesterday: streak from plate 3 (hPCD + BL01 + pSB1A3 1xGibson) showed no color, whereas streak from plate 7 (hPCD + BL01 + pSB1A3 1/4x Gibson), showed RFP expression. The pSB1A3 template carries RFP.
  • Grow 2x 2 mL cultures from plate 3 streak to investigate whether an insert replaced RFP.
  • Do Zymo minipreps

Gibson Re-transformation

  1. hPCD + BL01 + pSB1A3 (#3), 1xGibson, 6.0 μL
  2. pSB1A3 (#4), 1xGibson, 6.0 μL
  • Add to 50 μL cells; ice/ 10 min.
  • Plate on 100 μg/mL amp LB agar



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