Daniel:Notebook/ComboLock/2016-6-23: Difference between revisions

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>Djacobse
>Djacobse
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<li>Put 1 uL C1 Probe and 1 uL C2 probe into a 0.2 mL tube</li>
<li>Put 1 uL C1 Probe and 1 uL C2 probe into a 0.2 mL tube</li>
<li>Heat C probes to 90C for 5 min; Chill probes on ice to quench</li>
<li>Heat C probes to 90C for 5 min; Chill probes on ice to quench</li>
<li>Add probes to hybridization buffer for final concentration of 100 nM (0.5 uL/probe/sample using 0.5mL hybridization buffer)</li>
<li>Add probes to CP buffer for final concentration of 100 nM (Add 1 uL probe mixture to 0.5mL hybridization buffer)</li>
<li>Incubate probes at 40C for 1 hour with vigorous agitation</li>
<li>Incubate probes at 40C for 1 hour with vigorous agitation</li>
<li>Wash three times with wash buffer and pelleting at 600xg for 3 min</li>
<li>Wash three times with 200 uL wash buffer and pelleting at 600xg for 3 min</li>
<li>Incubate cells for 20 min at 40C in stringent wash buffer</li>
<li>Incubate cells for 20 min at 40C in 200 uL stringent wash buffer</li>
</ol>
</ol>
<li>Latch and Padlock Hybridization</li>
<li>Latch and Padlock Hybridization</li>
<ol type="A">
<ol type="A">
<li>Pellet at 600xg for 3 min</li>
<li>Pellet at 600xg for 3 min and remove supernatant</li>
<li>Incubate with 100 nM insert/backbone oligos for 30 min at 37C</li>
<li>Resuspend pellet in 50 uL hybridization buffer with 100 nM insert/backbone oligos for 30 min at 37C</li>
<li>Wash twice</li>
<li>Wash twice</li>
<ol type="a"><li>Wash by pelleting cells at 600xg for 3 min</li></ol></ol>
<ol type="a"><li>Wash by pelleting cells at 600xg for 3 min</li></ol></ol>
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</ol>
</ol>
</ol>
</ol>
</ol>
===Buffers===
<ol type="A">
<li>C-Probe (CP) Buffer</li>
<ol type="a">
<li>100 nM insert/backbone oligos</li>
<li>1X SSC</li>
<li>40 U/mL RNasin</li>
<li>PBS</li>
</ol>
<li>Wash Buffer</li>
<ol type="a">
<li>PBS</li>
<li>0.1% Tween</li>
<li>4 U/mL RNasin</li>
</ol>
</ol>

Revision as of 22:50, 22 June 2016

Stage 2 Test

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The purpose of this experiment is to test the latch and padlock binding, termed stage 2 (at the moment). This is based on the success of the VIM binding for both C-Probes and antibodies.

Protocol

Sample Matrix

Sample VIM-C1 (1 uL) VIM-C2 (1 uL)
Sample 1 X X
Sample 2    
  1. C-Probe Hybridization
    1. Split cells into 2 samples (1 mL methanol each)
    2. Pellet cells via centrifugation at 600g for 3 min
    3. Put 1 uL C1 Probe and 1 uL C2 probe into a 0.2 mL tube
    4. Heat C probes to 90C for 5 min; Chill probes on ice to quench
    5. Add probes to CP buffer for final concentration of 100 nM (Add 1 uL probe mixture to 0.5mL hybridization buffer)
    6. Incubate probes at 40C for 1 hour with vigorous agitation
    7. Wash three times with 200 uL wash buffer and pelleting at 600xg for 3 min
    8. Incubate cells for 20 min at 40C in 200 uL stringent wash buffer
  2. Latch and Padlock Hybridization
    1. Pellet at 600xg for 3 min and remove supernatant
    2. Resuspend pellet in 50 uL hybridization buffer with 100 nM insert/backbone oligos for 30 min at 37C
    3. Wash twice
      1. Wash by pelleting cells at 600xg for 3 min
  3. Circularization
    1. Prepare KLN mix with:
      1. 20% v/v HemoKlentaq
      2. 0.5 U/μL Ampligase
      3. 100 μM of dNTP mix
      4. 1x Ampligase Buffer
    2. Add 2 uL KLN mix to 20 uL of reaction
    3. Incubate at 55C for 4-20 hours
    4. Heat inactivate enzyme by incubating for 2 minutes at 94C
  4. Exonuclease Digestion
    1. Prepare exonuclease I/III mix by mixing exonuclease I (20 units/μL) and exonuclease III (200 units/μL) in 1:1 ratio
    2. Add 2 μL of exonuclease I/III mix to reaction
    3. Mix the reaction by swirling pipette around the well 5 times
    4. Incubate reaction at 37 ºC for 2 hours
    5. Heat inactivate enzyme by incubating at 94C for 5 minutes
  5. qPCR
    1. Set up reaction according to table
    2. qPCR Cycles
      1. 95C 3 min
      2. 95C 3 sec
      3. 55C 30 sec
      4. 72C 20 sec
      5. plate read
      6. goto b x20
      7. 72C 2 min
      8. 16C hold

Buffers

  1. C-Probe (CP) Buffer
    1. 100 nM insert/backbone oligos
    2. 1X SSC
    3. 40 U/mL RNasin
    4. PBS
  2. Wash Buffer
    1. PBS
    2. 0.1% Tween
    3. 4 U/mL RNasin