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

(Difference between revisions)
 Revision as of 17:37, 23 November 2012 (view source) (→11/21/12)← Previous diff Revision as of 17:48, 23 November 2012 (view source) (→11/21/12)Next diff → Line 123: Line 123: | DNA (clean digest) || 11.0 (~200 ng) | DNA (clean digest) || 11.0 (~200 ng) |- |- - | 10x buffer d.p. || 1.5 + | 10x phos. buffer || 1.5 |- |- | phosphatase || 0.5 | phosphatase || 0.5 Line 139: Line 139: '''Ligation''' '''Ligation''' * Use 20 ng of vector for each ligation = '''1.5 μL pSB1A3''' * Use 20 ng of vector for each ligation = '''1.5 μL pSB1A3''' - * Use 2x moles of H2B insert, relative to vector:  xμL  H2B insert = 3 * 410 bp H2B / 2000 bp pSB1A3 * 20 ng pSB1A3 / ### ng/μL H2B = '''### μL H2B''' + * Use 2x 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 2x moles of LOV insert, relative to vector:  xμL  LOV insert = 3 * 461 bp LOV / 2000 bp pSB1A3 * 20 ng pSB1A3 / ### ng/μL LOV = '''### μL LOV''' + * Use 2x 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''' Line 146: Line 146: |   || H2B || LOV  || Negative Control |   || H2B || LOV  || Negative Control |- |- - | Insert DNA (2x mol vector) || ### μL || ### || --- + | Insert DNA (2x mol vector) || 1.0 μL || 1.0 || --- || 1.0 || 1.0 || --- |- |- - | Vector DNA (50 ng) || 1.5  || 1.5 || 1.5 + | 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 + | 2x Roche Rapid Ligation buffer || 5.0 || 5.0 || 5.0 || 5.0 || 5.0 || 5.0 |- |- - | New England Biolabs T4 ligase || 1.0  || 1.0 || 1.0 + | T4 ligase || 1.0  NEB || 1.0 NEB || 1.0 NEB || 1.0 Roche || 1.0 Roche || 1.0 Roche |- |- - | dH2O || ### || ### || ### + | dH2O || 1.5 || 1.5 || 2.5 || 1.5 || 1.5 || 2.5 |- |- | TOTAL || 10.0 || 10.0 || 10.0 | TOTAL || 10.0 || 10.0 || 10.0

## Revision as of 17:48, 23 November 2012

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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

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 2x 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 2x 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 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 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