User:Karmella Haynes/Notebook/BioBrick cloning/2015/01/22: Difference between revisions

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Try different cDNA libraries for the ATF2 fragment to account for any mutations or deletions
Try different cDNA libraries for the ATF2 fragment to account for any mutations or deletions
# KAH60 "backbone" (without VP64, includes scars) = 6637: KAH60 F1/ KAH60 R1
# KAH60 "backbone" (without VP64, includes scars) = 6637: KAH60 F1/ KAH60 R1
# U2OS C002; ATF2 insert = 906: ATF2_f1/ ATF2_r1
# U2OS C002, 1:1000 dilution; ATF2 insert = 906: ATF2_f1/ ATF2_r1
# SKNSH C001; same
# SKNSH C001, 1:1000 dilution; same
# K562 C001; same
# K562 C001, 1:1000 dilution; same




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| bgcolor=#cfcfcf | Rxn3
| bgcolor=#cfcfcf | Rxn3
| bgcolor=#cfcfcf | Rxn4
| bgcolor=#cfcfcf | Rxn4
| rowspan="7" | [[Image:KAH012315_gel.jpg|270px|Hover name]]<br>10 μL/lane, 1% agarose; [http://openwetware.org/wiki/Image:KAH_Fermentas_GeneRuler_1kbplus.jpg Ladder]
| rowspan="7" | [[Image:KAH012315_gel.jpg|270px|Hover name]]<br>10 μL/lane, 1% agarose; [http://openwetware.org/wiki/Image:KAH_Fermentas_GeneRuler_1kbplus.jpg Ladder]
|-
|-
| Template || 0.2 KAH60/pcVN || 1.0 1:1000 U2OS cDNA || 1.0 1:1000 SKNSH cDNA || 1.0 1:1000 K562 cDNA
| Template || 0.2 KAH60/pcVN || 1.0 U2OS cDNA || 1.0 SKNSH cDNA || 1.0 K562 cDNA
|-
|-
| 10 uM fwd primer || 1.0 || 1.0 || 1.0 || 1.0
| 10 uM fwd primer || 1.0 || 1.0 || 1.0 || 1.0

Revision as of 10:36, 27 January 2015

Karmella's BioBrick Cloning <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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01/22/15

  • Gal4 fusion cloning


Planning: Gal4 fusion cloning

  • "Backbone" = Gal4-mCherry-VP64 construct KAH60/pcVN
  • Approach: swap-in activator domain to replace VP64
    • PCR-amplify backbone (omitting VP64)
    • PCR-amplify insert
    • Plan A: use LCR to ligate insert into backbone


Primers (ordered 01/02/15)
Attempt 1: swap-in ATF activation domain; add 5' phosphates to all oligos EXCEPT for bridging oligos

  • KAH60 "backbone" (without VP64, includes scars) = 6637
    • KAH60 F1
    • KAH60 R1
  • ATF2 insert = 906
    • ATF2_f1
    • ATF2_r1
  • LCR Bridging oligos
    • LCRb_KAH60_ATF2_1
    • LCRb_KAH60_ATF2_2


PCR-verify fragment primers
Try different cDNA libraries for the ATF2 fragment to account for any mutations or deletions

  1. KAH60 "backbone" (without VP64, includes scars) = 6637: KAH60 F1/ KAH60 R1
  2. U2OS C002, 1:1000 dilution; ATF2 insert = 906: ATF2_f1/ ATF2_r1
  3. SKNSH C001, 1:1000 dilution; same
  4. K562 C001, 1:1000 dilution; same


Reagent Rxn1 Rxn2 Rxn3 Rxn4 Hover name
10 μL/lane, 1% agarose; Ladder
Template 0.2 KAH60/pcVN 1.0 U2OS cDNA 1.0 SKNSH cDNA 1.0 K562 cDNA
10 uM fwd primer 1.0 1.0 1.0 1.0
10 uM rev primer 1.0 1.0 1.0 1.0
2x GoTaq green 12.5 12.5 12.5 12.5
dH2O 10.3 9.5 9.5 9.5
  25.0 25.0 25.0 25.0

Program: GOTAQ35cyc

  • 95°C, 3 min
  • 30x[95°C, 1 min; 57°C, 1 min; 72°C, 3 min]
  • 72°C, 3 min
  • 4°C ∞



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