Haynes Lab:Notebook/Investigating Photo-Switchable Synthetic Nucleosomes/2012/11/21

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==11/21/12==
==11/21/12==
 +
 +
'''Results from yesterday's ligation'''
 +
* Got 1:1 ratio of ligation: negative control for both
 +
* About 10 colonies total on every plate
 +
* Forgot to take into account X/S vector self-ligation
 +
* Will pick 4 colonies from each (H2B, LOV) to see if anything worked.
 +
* In the mean time, will retry cloning, trouble shoot procedure with help from Dr. Haynes
 +
 +
----
 +
* Repeat PCR of H2B and LOV inserts
* Repeat PCR of H2B and LOV inserts
Line 28: Line 38:
| dH<sub>2</sub>O || 10.0 || 10.0
| dH<sub>2</sub>O || 10.0 || 10.0
|-
|-
-
| Total || --- || ---
+
| Total || 25.0 || 25.0
|}
|}
Line 37: Line 47:
* 4°C ∞
* 4°C ∞
-
{| class="wikitable" border=0
+
* Clean up PCR products using the Zymo Clean and Concentrator kit
 +
* Be sure to elute using 15 μL dH<sub>2</sub>O
 +
 
 +
----
 +
 
 +
*'''[[User:Karmella Haynes|---Karmella]] 15:56, 21 November 2012 (EST)''': Digest, purification, and ligation
 +
 
 +
'''Assemblies'''
 +
# NEB T4 ligase; H2B - X/S - 410 bp + pSB1A3 - X/S - 2000 bp
 +
# NEB T4 ligase; LOV - X/S - 461 bp + pSB1A3 - X/S - 2000 bp
 +
# NEB T4 ligase; (negtaive control) pSB1A3 - X/S - 2000 bp
 +
# Roche T4 ligase; H2B - X/S - 410 bp + pSB1A3 - X/S - 2000 bp
 +
# Roche T4 ligase; LOV - X/S - 461 bp + pSB1A3 - X/S - 2000 bp
 +
# Roche T4 ligase; (negtaive control) pSB1A3 - X/S - 2000 bp
 +
 
 +
* Digests:
 +
** In a 30 μL reaction, cut H2B with XbaI and SpeI
 +
** In a 30 μL reaction, cut LOV with XbaI and SpeI
 +
 
 +
{| class="wikitable" border=1 cellpadding="5" cellspacing="0"
|-
|-
-
| <u>Expected:</u><br>1. H2B = 410 <br>2. LOV = 461
+
| Reagent || H2B PCR || LOV PCR
-
| <br>
+
|-
 +
| DNA || 15.0 || 15.0
 +
|-
 +
| XbaI || 1.0|| 1.0
 +
|-
 +
| SpeI || 1.0 || 1.0
 +
|-
 +
| 10x buffer || 3.0 || 3.0
 +
|-
 +
| dH<sub>2</sub>O || 10.0 || 10.0
 +
|-
 +
| Total vol. || 30. 0 || 30.0
|}
|}
-
<center>
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-
[[Image:Gel_11-9-12.png|Results of the digests are shown.]]
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* Run entire 30 μL on a 1% gel (use the big fat-tooth well comb)
 +
* Cut band out of gel (use UV box)
 +
 
 +
 
 +
Results from gel recovery:
 +
{| class="wikitable" border=1 cellpadding="5" cellspacing="0"
 +
|-
 +
| Sample|| 260|| 260/280 || ng/μL
 +
|-
 +
| H2B - X/S 1 || 0.016 ||1.807|| 15.961
 +
|-
 +
| H2B - X/S 2 || 0.009 || 1.976 || 8.619
 +
|-
 +
| LOV - X/S 1 || 0.006|| 1.694 || 6.455
 +
|-
 +
| LOV - X/S 2 || 0.025|| 1.883 || 25.363
 +
|}
 +
 
 +
 
 +
[[Image:VN_Gel_11-21-12.png|Results of from the digests are shown.]]
[[Image:KAH_Fermentas_GeneRuler_1kbplus.jpg]]
[[Image:KAH_Fermentas_GeneRuler_1kbplus.jpg]]
-
</center>
 
-
<center>
+
# H2B = 410
-
Results of the PCR product digests are shown, with H2B on the left and LOV on the right. The gel was loaded with 5 μL samples.
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# LOV = 461
-
</center>
+
 
 +
* There were two samples made of each PCR reaction.  The two from the H2B are shown on the left, and the two from the LOV are shown on the right.
 +
 
 +
 
 +
'''Dephosphorylation''' (11/23/12)
 +
 
 +
> Dephosphorylation (Roche)
 +
# pSB1A3 - X/S = 2000 bp
 +
 
 +
{| class="wikitable" border="0" cellspacing="3" <!-- Dephos table -->
 +
|-
 +
| <u>Reagent</u> || <u>Volume</u>
 +
|-
 +
| DNA (clean digest) || 11.0 (~200 ng)
 +
|-
 +
| 10x phos. buffer || 1.5
 +
|-
 +
| phosphatase || 0.5
 +
|-
 +
| dH<sub>2</sub>O || 2.0
 +
|-
 +
| &nbsp; || 15 μL
 +
|}
 +
 
 +
* Incubate at 37°C/ 10 min.
 +
* Heat inactivate at 75°C/ 2 min.
 +
* [final] = 200 ng/μL / 15 μL = ~13 ng/μL
 +
 
 +
 
 +
'''Ligation'''
 +
* Use 20 ng of vector for each ligation = '''1.5 μL pSB1A3'''
 +
* Use 3x moles of H2B insert, relative to vector:  xμL  H2B insert = 3 * 410 bp H2B / 2000 bp pSB1A3 * 20 ng pSB1A3 / 16 ng/μL H2B = at least '''0.8 μL H2B'''
 +
* Use 3x moles of LOV insert, relative to vector:  xμL  LOV insert = 3 * 461 bp LOV / 2000 bp pSB1A3 * 20 ng pSB1A3 / 25 ng/μL LOV = at least '''0.5 μL LOV'''
 +
 
 +
 
 +
{| class="wikitable" width=700px
 +
| &nbsp; || H2B || LOV  || Negative Control || H2B || LOV  || Negative Control
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|-
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| Insert DNA (2x mol vector) || 1.0 μL || 1.0 || --- || 1.0 || 1.0 || ---
 +
|-
 +
| Vector DNA (50 ng) || 1.5  || 1.5 || 1.5 || 1.5  || 1.5 || 1.5
 +
|-
 +
| 2x Roche Rapid Ligation buffer || 5.0 || 5.0 || 5.0 || 5.0 || 5.0 || 5.0
 +
|-
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| T4 ligase || 1.0  NEB || 1.0 NEB || 1.0 NEB || 1.0 Roche || 1.0 Roche || 1.0 Roche
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|-
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| dH<sub>2</sub>O || 1.5 || 1.5 || 2.5 || 1.5 || 1.5 || 2.5
 +
|-
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| TOTAL || 10.0 || 10.0 || 10.0  || 10.0 || 10.0 || 10.0
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|-
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| colspan="3" | Mix the reaction(s) thoroughly by flicking the tube.<br>Incubate at room temperature for 10 minutes.
 +
|}
 +
 
 +
Proceed directly to Transformation. See http://openwetware.org/wiki/Haynes:Assembly101
 +
 

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11/21/12

Results from yesterday's ligation

  • Got 1:1 ratio of ligation: negative control for both
  • About 10 colonies total on every plate
  • Forgot to take into account X/S vector self-ligation
  • Will pick 4 colonies from each (H2B, LOV) to see if anything worked.
  • In the mean time, will retry cloning, trouble shoot procedure with help from Dr. Haynes


  • Repeat PCR of H2B and LOV inserts
  • Note: Primers add a XbaI site upstream and the SpeI, NotI, and PstI sites downstream
  1. H2B-GFP plasmid + BB_H2B fwd + BB_H2B rev
  2. LOV plasmid + BB_LOV fwd + BB_LOV rev
Reagents H2B LOV
Plasmid DNA 0.5 μL 0.5
primer 1 (10 μM) 1.0 1.0
primer 2 (10 μM) 1.0 1.0
2x GoTaq mix 12.5 12.5
dH2O 10.0 10.0
Total 25.0 25.0

PCR program:

  • 95°C, 3 min.
  • [95°C, 30 sec; 57°C, 30 sec.; 72°C, 30 sec.] x35 cycles
  • 72°C, 3 min.
  • 4°C ∞
  • Clean up PCR products using the Zymo Clean and Concentrator kit
  • Be sure to elute using 15 μL dH2O
  • ---Karmella 15:56, 21 November 2012 (EST): Digest, purification, and ligation

Assemblies

  1. NEB T4 ligase; H2B - X/S - 410 bp + pSB1A3 - X/S - 2000 bp
  2. NEB T4 ligase; LOV - X/S - 461 bp + pSB1A3 - X/S - 2000 bp
  3. NEB T4 ligase; (negtaive control) pSB1A3 - X/S - 2000 bp
  4. Roche T4 ligase; H2B - X/S - 410 bp + pSB1A3 - X/S - 2000 bp
  5. Roche T4 ligase; LOV - X/S - 461 bp + pSB1A3 - X/S - 2000 bp
  6. Roche T4 ligase; (negtaive control) pSB1A3 - X/S - 2000 bp
  • Digests:
    • In a 30 μL reaction, cut H2B with XbaI and SpeI
    • In a 30 μL reaction, cut LOV with XbaI and SpeI
Reagent H2B PCR LOV PCR
DNA 15.0 15.0
XbaI 1.0 1.0
SpeI 1.0 1.0
10x buffer 3.0 3.0
dH2O 10.0 10.0
Total vol. 30. 0 30.0


  • Run entire 30 μL on a 1% gel (use the big fat-tooth well comb)
  • Cut band out of gel (use UV box)


Results from gel recovery:

Sample 260 260/280 ng/μL
H2B - X/S 1 0.016 1.807 15.961
H2B - X/S 2 0.009 1.976 8.619
LOV - X/S 1 0.006 1.694 6.455
LOV - X/S 2 0.025 1.883 25.363


Results of from the digests are shown. Image:KAH_Fermentas_GeneRuler_1kbplus.jpg

  1. H2B = 410
  2. LOV = 461
  • There were two samples made of each PCR reaction. The two from the H2B are shown on the left, and the two from the LOV are shown on the right.


Dephosphorylation (11/23/12)

> Dephosphorylation (Roche)

  1. pSB1A3 - X/S = 2000 bp
Reagent Volume
DNA (clean digest) 11.0 (~200 ng)
10x phos. buffer 1.5
phosphatase 0.5
dH2O 2.0
  15 μL
  • Incubate at 37°C/ 10 min.
  • Heat inactivate at 75°C/ 2 min.
  • [final] = 200 ng/μL / 15 μL = ~13 ng/μL


Ligation

  • Use 20 ng of vector for each ligation = 1.5 μL pSB1A3
  • Use 3x moles of H2B insert, relative to vector: xμL H2B insert = 3 * 410 bp H2B / 2000 bp pSB1A3 * 20 ng pSB1A3 / 16 ng/μL H2B = at least 0.8 μL H2B
  • Use 3x moles of LOV insert, relative to vector: xμL LOV insert = 3 * 461 bp LOV / 2000 bp pSB1A3 * 20 ng pSB1A3 / 25 ng/μL LOV = at least 0.5 μL LOV


  H2B LOV Negative Control H2B LOV Negative Control
Insert DNA (2x mol vector) 1.0 μL 1.0 --- 1.0 1.0 ---
Vector DNA (50 ng) 1.5 1.5 1.5 1.5 1.5 1.5
2x Roche Rapid Ligation buffer 5.0 5.0 5.0 5.0 5.0 5.0
T4 ligase 1.0 NEB 1.0 NEB 1.0 NEB 1.0 Roche 1.0 Roche 1.0 Roche
dH2O 1.5 1.5 2.5 1.5 1.5 2.5
TOTAL 10.0 10.0 10.0 10.0 10.0 10.0
Mix the reaction(s) thoroughly by flicking the tube.
Incubate at room temperature for 10 minutes.

Proceed directly to Transformation. See http://openwetware.org/wiki/Haynes:Assembly101




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