Daniel:Notebook/ComboLock/2017-2-27: Difference between revisions

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Repeating the circularization and RCA test using the three different polymerase enzymes to classify which is best to use. This will use the C4-C2 template, which is the simplified template that is the equivalent of the two C probe arms ligated and gap-filled.
Repeating the circularization and RCA test using the three different polymerase enzymes to classify which is best to use. This will use the C4-C2 template, which is the simplified template that is the equivalent of the two C probe arms ligated and gap-filled.


==Protocol==
==Protocol-Part 1==
 
'''Sample Matrix'''
 
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext>
|- style="background-color:#B1A0C7;font-size:12pt;font-weight:bold" align="center"
| width="120" height="28" | Sample
| width="190" | Condition
 
|- style="font-size:12pt"
| height="15"  valign="bottom" | Sample 1 (ABC)
| align="center" valign="bottom" | Sample
 
|- style="background-color:#BFBFBF;font-size:12pt"
| height="15"  valign="bottom" | Sample 2 (ABC)
| align="center" valign="bottom" | No Padlock PO4
 
|}


<ol>
<ol>
Line 32: Line 49:


|- style="font-size:12pt"
|- style="font-size:12pt"
| height="15"  valign="bottom" | PCCB-02
| height="15"  valign="bottom" | Padlock0501
| align="center" | 10 uM
| align="center" | 10 uM
| align="center" | 100 pmol total
| align="center" | 100 pmol total
Line 72: Line 89:
<li>Padlock Hybridization</li>
<li>Padlock Hybridization</li>
<ol type="A">
<ol type="A">
<li>Make 2 of the following master mix</li>
<li>Make following 6.1X master mixes</li>
<ol type="a">
 
<li>8.2 uL 10 uM padlock0501</li>
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext>
<li>8.2 uL Amp Ligase 10X reaction buffer</li>
|- style="background-color:#DA9694;font-size:12pt;font-weight:bold" align="center"
<li>65.6 uL nfH2O</li></ol>
| width="150" height="39" | Reagent
<li>Resuspend sample in 20 uL 1X Amp Ligase buffer</li>
| width="85" | MM1 (uL)
<li>Incubate at 37C for 30 minutes</li></ol>
| width="85" | MM2 (uL)
******
 
|- style="font-size:12pt"
| height="15"  valign="bottom" | Padlock0501
| align="center" align="center" valign="bottom" | 0
| align="center" align="center" valign="bottom" | 3.1
 
|- style="background-color:#BFBFBF;font-size:12pt"
| height="15"  valign="bottom" | PNK Reaction
| align="center" align="center" valign="bottom" | 6.2
| align="center" align="center" valign="bottom" | 0
 
|- style="font-size:12pt"
| height="15"  valign="bottom" | Amp Ligase Buffer
| align="center" align="center" valign="bottom" | 6.2
| align="center" align="center" valign="bottom" | 6.2
 
|- style="background-color:#BFBFBF;font-size:12pt"
| height="15"  valign="bottom" | nfH2O
| align="center" align="center" valign="bottom" | 49.6
| align="center" align="center" valign="bottom" | 52.7
 
|- style="font-size:12pt"
| height="15"  valign="bottom" | Total
|style="font-weight:bold" align="center" align="center" valign="bottom" | 62
|style="font-weight:bold" align="center" align="center" valign="bottom" | 62
 
|}
 
<li>Resuspend sample in 20 uL padlock buffer</li>
<li>Incubate at 37C for 30 minutes</li>
<li>Wash twice with wash buffer</li></ol>
</ol>
 
==Protocol-Part 2==
 
<ol start="4">
<li>Circularization</li>
<li>Circularization</li>
<ol type="A">
<ol type="A">
<li>Prepare 8.5X uL Phusion mix</li>
<li>Prepare 6.5X uL Phusion mix</li>


{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext>
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext>
|- style="background-color:#C4D79B;font-size:12pt;font-weight:bold" align="center"
|- style="background-color:#C4D79B;font-size:12pt;font-weight:bold" align="center"
| width="140" height="30" | Reagent
| width="190" height="30" | Reagent
| width="65" | Stock Conc
| width="65" | Stock Conc
| width="65" | Final Amount
| width="65" | Final Amount
| width="65" | 1x Vol (uL)
| width="65" | 1x Vol (uL)
| width="65" | MM Vol (8.5x) (uL)
| width="105" | MM Vol (6.5x) (uL)


|- style="font-size:12pt"
|- style="font-size:12pt"
Line 97: Line 149:
| align="center" | 40 nmol
| align="center" | 40 nmol
| align="center" align="center" | 8
| align="center" align="center" | 8
| align="center" align="center" | 68
| align="center" align="center" | 52


|- style="background-color:#BFBFBF;font-size:12pt"
|- style="background-color:#BFBFBF;font-size:12pt"
Line 104: Line 156:
| align="center" | 600 pmol
| align="center" | 600 pmol
| align="center" align="center" | 0.6
| align="center" align="center" | 0.6
| align="center" align="center" | 5.1
| align="center" align="center" | 3.9


|- style="font-size:12pt"
|- style="font-size:12pt"
Line 111: Line 163:
| align="center" | 15 umol
| align="center" | 15 umol
| align="center" align="center" | 3
| align="center" align="center" | 3
| align="center" align="center" | 25.5
| align="center" align="center" | 19.5


|- style="background-color:#BFBFBF;font-size:12pt"
|- style="background-color:#BFBFBF;font-size:12pt"
Line 118: Line 170:
| align="center" | 1X
| align="center" | 1X
| align="center" align="center" | 2
| align="center" align="center" | 2
| align="center" align="center" | 17
| align="center" align="center" | 13


|- style="font-size:12pt"
|- style="font-size:12pt"
Line 125: Line 177:
| align="center" | 10 U
| align="center" | 10 U
| align="center" align="center" | 2
| align="center" align="center" | 2
| align="center" align="center" | 17
| align="center" align="center" | 13


|- style="background-color:#BFBFBF;font-size:12pt"
|- style="background-color:#BFBFBF;font-size:12pt"
Line 132: Line 184:
| align="center" | 6.4U
| align="center" | 6.4U
| align="center" align="center" | 3.2
| align="center" align="center" | 3.2
| align="center" align="center" | 27.2
| align="center" align="center" | 20.8


|- style="font-size:12pt"
|- style="font-size:12pt"
Line 139: Line 191:
| align="center" align="center" | &nbsp;
| align="center" align="center" | &nbsp;
| align="center" align="center" | 1.2
| align="center" align="center" | 1.2
| align="center" align="center" | 8.4
| align="center" align="center" | 7.8


|- style="background-color:#BFBFBF;font-size:12pt"
|- style="background-color:#BFBFBF;font-size:12pt"
Line 146: Line 198:
| align="center" align="center" | &nbsp;
| align="center" align="center" | &nbsp;
|style="font-weight:bold" align="center" align="center" | 20
|style="font-weight:bold" align="center" align="center" | 20
|style="font-weight:bold" align="center" align="center" | 140
|style="font-weight:bold" align="center" align="center" | 130


|}
|}


<li>Add 20 uL phusion mix to 20 uL reaction</li>
<li>Add 20 uL phusion mix to 20 uL reaction</li>
<li>Incubate at 40C for 4 hours</li>
<li>Incubate at 55C for 2 hours</li>
</ol>
</ol>
<li>Exonuclease Digestion</li>
<ol type="A">
<li>Mix 12.5 uL Exo I (20U/uL) and 2.5 uL ExoIII (100U/uL)</li>
<li>Add 2 uL to each sample, mix by swirling pipette tip</li>
<li>Incubate for 1 hour at 37C</li>
<li>Heat kill by incubating for 5 min at 95C</li>
</ol></ol>
Continued [[Daniel:Notebook/ComboLock/2017-2-28|tomorrow]]


Continued [[Daniel:Notebook/ComboLock/2017-1-7|tomorrow]]
[[Category:ComboLock]] [[Category:20170227]]

Latest revision as of 22:51, 27 February 2017

RCA + Circularization Test[edit]

Back to Calendar

Repeating the circularization and RCA test using the three different polymerase enzymes to classify which is best to use. This will use the C4-C2 template, which is the simplified template that is the equivalent of the two C probe arms ligated and gap-filled.

Protocol-Part 1[edit]

Sample Matrix

Sample Condition
Sample 1 (ABC) Sample
Sample 2 (ABC) No Padlock PO4
  1. Phosphorylation-Padlock0501
    1. Set up reaction according to table
    2. Reagent Stock Conc Final Conc./Amount uL added
      T4 Polynucleotide Kinase Buffer 10X 1X 2
      ATP 10 mM 1 mM 2
      Padlock0501 10 uM 100 pmol total 10
      T4 DNA Kinase 10 U/uL 10 U 1
      nfH2O NA NA 5
      Total     20
    3. Incubate at 37C for 30 min
    4. Heat kill enzyme with 15 minutes at 65C
  2. Template-Bead Binding
    1. Suspend 2 uL (8 ug) beads per sample in 100 uL wash buffer
    2. Apply magnet for 30 sec and remove supernatant
    3. Dilute 5 uL C4-C2 template into 45 uL nfH2O
    4. Add 2 uL diluted template per sample to bead solution; incubate at RT for 5 min
    5. Wash beads with 100 uL wash buffer; vortex to suspend; apply magnet and remove supernatant
  3. Padlock Hybridization
    1. Make following 6.1X master mixes
    2. Reagent MM1 (uL) MM2 (uL)
      Padlock0501 0 3.1
      PNK Reaction 6.2 0
      Amp Ligase Buffer 6.2 6.2
      nfH2O 49.6 52.7
      Total 62 62
    3. Resuspend sample in 20 uL padlock buffer
    4. Incubate at 37C for 30 minutes
    5. Wash twice with wash buffer

Protocol-Part 2[edit]

  1. Circularization
    1. Prepare 6.5X uL Phusion mix
    2. Reagent Stock Conc Final Amount 1x Vol (uL) MM Vol (6.5x) (uL)
      NAD+ 5 mM 40 nmol 8 52
      dNTP 1 mM 600 pmol 0.6 3.9
      Betaine 5 M 15 umol 3 19.5
      10X AmpLigase Buffer 10X 1X 2 13
      Amp Ligase 5 U/uL 10 U 2 13
      Phusion HF DNA Polymerase 2000 U/mL 6.4U 3.2 20.8
      nf H2O     1.2 7.8
      Total     20 130
    3. Add 20 uL phusion mix to 20 uL reaction
    4. Incubate at 55C for 2 hours
  2. Exonuclease Digestion
    1. Mix 12.5 uL Exo I (20U/uL) and 2.5 uL ExoIII (100U/uL)
    2. Add 2 uL to each sample, mix by swirling pipette tip
    3. Incubate for 1 hour at 37C
    4. Heat kill by incubating for 5 min at 95C

Continued tomorrow