Team:Lethbridge/Notebook/Lab Work/June

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June 2010

June 1/2010

JV quantified the amount of DNA in gels run to date using ImageJ software. Results to be posted in working plasmids box.

Objective: Transform plasmids into DH5α
Method: Follow competent cell transformation protocol to transform the following:
From our ligations:

pLacI-sRBS-Lumazine-dT
pLacI-sRBS-Lumazine-dT
mms6 (A6)
mms6 (B6)
xylE (C4)
xylE (B4)

From the 2010 Parts Distribution:

ECFP (Bba_E0020)
EYFP (Bba_E0030)
BglII Endonuclease (Bba_K112106)

June 2/2010

(In Lab: JV)

Objective: Isolate plasmid DNA of RBS-xylE (BBa_J33204) from DH5α cells and confirm results.

Method: "Mini-prep" the plasmid DNA using boiling lysis miniprep. Then restrict the DNA once and run on a 1% agarose gel (TAE).

Restriction Reaction

Ingredient	Volume(µL)
MilliQ H₂0 Water	15.75
Orange Buffer (10x)	2
pDNA (rbs-xylE)	2
EcoRI	0.25

Unrestricted Control

Ingredient	Volume(µL)
MilliQ H₂0 Water	16
Orange Buffer (10x)	2
pDNA (rbs-xylE)	2

DNA was restricted for 80 minutes at 37^oC.

Analyzed results on a 1% agarose gel. Load order as follows:

Lane	Sample	Volume Sample (µL)	Volume Loading Dye (µL)
1	Restricted RBS-xylE	10	2
1	Unestricted RBS-xylE^†	1	2
1	1kb Ladder^†^†	2	2

† Added 9µL MilliQ H₂O
†† Added 8µL MilliQ H₂O
Ran gel at 100V from 2 hours.
Results:

Conclusions: Plasmid DNA prep and restriction was successful.

Objective: Ligate rbs-xylE (Bba_J33204) to our double terminator, and insert it into the pSB1T3 plasmid backbone.
Method:

Restrictions
- Restrict rbs-xylE wit EcoRI and SpeI (Red Buffer)
- Restrict the double terminator with XbaI and PstI (Tango Buffer)
- Restrict pSB1T3 with EcoRI and PstI (Red Buffer)
Set up reactions as follows:

Component Volume (µL)

MilliQ H₂O 15.5

Buffer 2

pDNA 2

Enzyme 0.25 + 0.25

Set up control reaction as follows:
- MilliQ H₂O - 16µL
- Buffer - 2µL
- pDNA - 2µL
Incubated reactions for 65 minutes at 37^oC
Killed enzymes by incubating reactions for 10 minutes at 65^oC

Ligation
Reaction set up as follows:

T4 DNA ligase - 0.25µL
rbs-xylE - 5µL
dT - 3µL
pSB1T3 - 8µL
10x Ligation Buffer - 2µL
MilliQ H₂O - 1.75µL

Incubated reactions overnight at room temperature (total of 19.5 hours)
Killed enzymes by incubating reactions for 10 minutes at 80^oC</ul>

June 2/2010 - Evening

Objective: Set up new ligations of pLacI and sRBS-Lum-dT according to Tom Knight's protocol. Previous ligation had very little DNA.
Relevant Information:

Want a final mass of 25ng of each pDNA in the ligation mix.
Final concentration of pDNA in restriction digest should be 25-50ng/µL.
Tom Knight's restriction reaction is 50µL, therefore there should be 1000ng pDNA in each restriction digest.
Identified the following plasmids in our working plasmids box:

Common Name	Location	Concentration (ng/µL)	Volume/rxn (µL)
pLacI Maxiprep	A9	990	~1
pLacI (B1)	A6	440	~2
sRBS-Lum-dT (2)	A1	965	~1
sRBS-Lum-dT (1)	A2	1145	~1
sRBS-Lum-dT Maxiprep	B8	4780	~.2
sRBS-Lum-dT	B7	4375	~.25
sRBS-Lum-dT (1)	G2	335	~3
sRBS-Lum-dT (2)	G3	965	~2

Make a 1:10 dilution of sRBS-Lum-dt maxiprep (D8) and sRBS-Lum-dT (B7). 0.5µL pDNA in 4.5µL water.
Cut pLacI with EcoRI and SpeI
Cut sRBS-Lum-dT with XbaI and PstI
Cut pSB1T3 with EcoRI and PstI
Will have total of 12 ligation reactions, want 12x2µL of pSB1T3 to add to each, therefore want 25µL of pSB1T3.

Method:
Restriction

Name	[pDNA] (ng/µL)	Volume pDNA (µL)	Volume Water (µL)	Volume Buffer (µL)	Enzymes	Total Volume
sRBS-Lum-dT (A1)	965	1	43.5	5	0.25µL XbaI 0.25µL PstI	50
sRBS-Lum-dT (A2)	1145	1	43.5	5	0.25µL XbaI 0.25µL PstI	50
pLacI Maxiprep (A1)	990	1	43.5	5	0.25µL EcoRI 0.25µL SpeI	50
sRBS-Lum-dT Maxiprep(B8)	4780	2 (of 1:10 dilution)	42.5	5	0.25µL XbaI 0.25µL PstI	50
sRBS-Lum-dT (B7)	4375	2.5 (of 1:10 dilution)	42	5	0.25µL XbaI 0.25µL PstI	50
pLacI (D6)	440	2	42.5	5	0.25µL EcoRI 0.25µL SpeI	50
sRBS-Lum-dT (G2)	335	3	41.5	5	0.25µL XbaI 0.25µL PstI	50
sRBS-Lum-dT (G3)	540	2	42.5	5	0.25µL XbaI 0.25µL PstI	50
pSB1T3	25	12.5	7	5	0.25µL EcoRI 0.25µL PstI	50

Incubate for 30 minutes at 37^oC (Start- 12:10pm; End- 12:40pm)
Heat kill enzymes at 80^oC for 20 minutes

Ligation:
In a 10µL final volume, add:

2µL of sRBS-Lum-dT component
2µL of pLacI component
2µL of pSB1T3 component
1µL of T4 Buffer
0.25µL of T4 DNA Ligase
2.75µL of MilliQ H₂O

Incubate for 30 minutes at room temperature to ligate
Incubate for 20 minutes at 80^oC to heat kill

June 3/2010

Carried out protocol described in June 2/2010 - Evening
Analyzed results on 1% agarose gel.Load order as follows:

Lane	Gel 1 Sample	Gel 1 Load	Gel 2 Sample	Gel 2 Load
1	1kb Ladder	2µL dye, 2µL ladder 8µL MilliQ H₂O	1kb Ladder	2µL dye, 2µL ladder 8µL MilliQ H₂O
2	Restricted sRBS-Lum-dT (A1)	10µL DNA 2µL Dye	pSB1T3 Ligation of: pLacI(A9)+sRBS-Lum-dT(A1)	10µL DNA 2µL Dye
3	Unrestricted sRBS-Lum-dT (A1)	10µL DNA 2µL Dye	pSB1T3 Ligation of: pLacI(D6)+sRBS-Lum-dT(A1)	10µL DNA 2µL Dye
4	Restricted sRBS-Lum-dT (A2)	10µL DNA 2µL Dye	pSB1T3 Ligation of: pLacI(A9)+sRBS-Lum-dT(A2)	10µL DNA 2µL Dye
5	Unrestricted sRBS-Lum-dT (A2)	10µL DNA 2µL Dye	pSB1T3 Ligation of: pLacI(D6)+sRBS-Lum-dT(A2)	10µL DNA 2µL Dye
6	Restricted sRBS-Lum-dT (B8)	10µL DNA 2µL Dye	pSB1T3 Ligation of: pLacI(A9)+sRBS-Lum-dT(B7)	10µL DNA 2µL Dye
7	Unrestricted sRBS-Lum-dT (B8)	10µL DNA 2µL Dye	pSB1T3 Ligation of: pLacI(D6)+sRBS-Lum-dT(B7)	10µL DNA 2µL Dye
8	Restricted sRBS-Lum-dT (B7)	10µL DNA 2µL Dye	pSB1T3 Ligation of: pLacI(A9)+sRBS-Lum-dT(G2)	10µL DNA 2µL Dye
9	Unrestricted sRBS-Lum-dT (B7)	10µL DNA 2µL Dye	pSB1T3 Ligation of: pLacI(D6)+sRBS-Lum-dT(G2)	10µL DNA 2µL Dye
10	Restricted sRBS-Lum-dT (G2)	10µL DNA 2µL Dye	pSB1T3 Ligation of: pLacI(D6)+sRBS-Lum-dT(G3)	10µL DNA 2µL Dye
11	Unrestricted sRBS-Lum-dT (G2)	10µL DNA 2µL Dye	pSB1T3 Ligation of: pLacI(A9)+sRBS-Lum-dT(G3)	10µL DNA 2µL Dye
12	Restricted sRBS-Lum-dT (G3)	10µL DNA 2µL Dye	pSB1T3 Ligation of: pLacI(D6)+sRBS-Lum-dT(B8)	10µL DNA 2µL Dye
13	Unrestricted sRBS-Lum-dT (G3)	10µL DNA 2µL Dye	pSB1T3 Ligation of: pLacI(A9)+sRBS-Lum-dT(B8)	10µL DNA 2µL Dye
14	Restricted pLacI (A9)	10µL DNA 2µL Dye	Restricted rbs-xylE	10µL DNA 2µL Dye
15	Unrestricted pLacI (A9)	10µL DNA 2µL Dye	Unrestricted rbs-xylE	10µL DNA 2µL Dye
16	Restricted pLacI B1 (D6)	10µL DNA 2µL Dye	Restricted pSB1T3	10µL DNA 2µL Dye
17	Unrestricted pLacI B1 (D6)	10µL DNA 2µL Dye	Unrestricted pSB1T3	10µL DNA 2µL Dye
18	Unrestricted dT	10µL DNA 2µL Dye	pSB1T3 Ligation of: rbs-xylE+dT	10µL DNA 2µL Dye
19	Restricted dT	10µL DNA 2µL Dye

Ran gel at 100V for 90 minutes.
Results:

Conclusions:

June 3/2010 - Evening

Objective: Repeat restriction of pSB1T3 and ligate with pLacI and sRBS-Lum-dT. Previous ligations all used up on gel.
Method:
Ligation:
In a 10µL final volume, add:

2µL of sRBS-Lum-dT component
2µL of pLacI component
2µL of pSB1T3 component
1µL of T4 Buffer
0.25µL of T4 DNA Ligase
2.75µL of MilliQ H₂O

Incubate for 30 minutes at room temperature to ligate
Incubate for 20 minutes at 80^oC to heat kill
Following ligation, transformed using transformation protocol. Plates incubated in 37^oC incubator for 44 hours.
Results: Only plate pLacI (D6) + sRBS-Lum-dT (G2) + pSB1T3 grew; had 2 colonies. Control plate did not grow, acidentally plated on tetracycline plate instead of ampicillin (pUC19).
Follow-up: Inoculated 5mL LB media (tetracycline positive) with cells from the transformation plates and incubated at 37^oC overnight. (June 5/2010).

Objective: Ligate pBad-TetR part with fluorescent protein part in pSB1C3 backbone.
Method:
Restriction

Name	Volume pDNA (µL)	Volume Water (µL)	Volume Buffer (µL)	Enzymes	Total Volume
pSB-NEYFP (B4)	.8	43.7	5	0.25µL XbaI 0.25µL PstI	50
pSB-CEYFP (B5)	.9	43.6	5	0.25µL XbaI 0.25µL PstI	50
pBad-TetR)	.3	44.2	5	0.25µL EcoRI 0.25µL SpeI	50
NEYFP (E1)	4.3	40.7	5	0.25µL XbaI 0.25µL PstI	50
NEYFP (E2)	0.3	42.2	5	0.25µL XbaI 0.25µL PstI	50
Fusion CEYFP (E3)	3.9	40.6	5	0.25µL XbaI 0.25µL PstI	50
Fusion CEYFP (E4)	2.0	42.5	5	0.25µL XbaI 0.25µL PstI	50
Fusion CEYFP (E5)	3.0	41.5	5	0.25µL XbaI 0.25µL PstI	50
CEYFP (E6)	0.6	43.9	5	0.25µL XbaI 0.25µL PstI	50
CEYFP (E7)	0.5	44.0	5	0.25µL XbaI 0.25µL PstI	50
pBad-TetR (F4)	2.5	42	5	0.25µL EcoRI 0.25µL SpeI	50
pBad-TetR (F5)	1.7	42.8	5	0.25µL EcoRI 0.25µL SpeI	50
pSB-CEYFP (G4)	2.9	41.6	5	0.25µL XbaI 0.25µL PstI	50
pSB1C3	15.5	46		0.25µL EcoRI 0.25µL PstI	62

Incubated at 37^oC for 75 minutes.

Used Red buffer for the EcoRI/SpeI and EcoRI/PstI digests
Used Tango buffer for the XbaI/PstI digests
Did not heat kill upon removal from incubation, put directly into -20^oC fridge.

Continue Ligation on Saturday (See below).

June 5/2010

(In the lab:AS)
Objective: Ligate restriction products from June 3/2010.
Relevant information:

Have 3 tubes of part 1 (pBad-TetR)
- In ampicillin backbone
Have 10 tubes of part 2 (fluorescent protein - various)
- In ampicillin backbone
Will have 30 combinations
Will use pSB1C3 as plasmid backbone
- Used most of the pSB1T3 and want to save remainder for creating new backbone via PCR.

Method:
*Restriction digests were not heat killed after reactions. Freezing probably killed the restriction enzymes, but I will hea kill them at 80^oC for 20 minutes anyways prior to adding Ligase.

- Cool on ice for 10 minutes before adding ligase.

Master Mix	Volume/tube (µL)	Total Volume (µL)
DNA	6	---
10x Buffer	1	32
T4 DNA Ligase	.25	8
MilliQ H₂O	2.75	88

Add 4µL master mix to each DNA tube.

Follow-up: Ligation reactions will be transformed into DH5α cells

June 6/2010

(In Lab: JV, HS)

Objective:
Isolate the following plasmid DNA from DH5α:

pLacI-sRBS-Lumazine-dT in pSB1T3 (colony 2)
pLacI-sRBS-Lumazine-dT in pSB1T3 (colony 1)

Method:
Followed boiling lysis miniprep protocol. Eluted with 10µL Milli-Q H₂O and RNase A.

Notes:

Placed colony 2 in cell E10 of glycerol stocks and J6 of working plasmid box.
Placed colony 2 in cell F1 of glycerol stocks and J5 of working plasmid box.

Objective:
Transformed the following plasmid DNA into DH5α cells:

pBad-TetR-CEYFP: (F5+E6), (B10+E7), (B10+E6), (F4+E6), (F5+E4), (F4+E7)
pBad-TetR-Fusion CEYFP: (F5+E3), (B10+E4), (F4+E3), (B10+E3), (B10+E5), (F4+E4), (F5+E4), (F5+E5), (F4+E5)
pBad-TetR-pSB CEYFP: (F4+B5), (B10+G4), (F4+G4), (F4+B5), (F5+B5), (F5+G4)
pBad-TetR-NEYFP: (F5+E1), (B10+E1), (F4+E2), (F5+E2), (B10+E2), (F4+E1)
pBad-TetR-pSB NEYFP: (F5+B4), (F4+B4), (B10+B4)

Positive control -> DH5α + pSB1C3
Negative control -> DH%α + Milli-Q H₂O

Method:
Followed Competent Cell Transformation protocol and used chloramphenicol as an antibiotic. We plated all 200µL of DNA onto the plates. The plates were incubated at 37^oC from 4:30pm to 10:00am.

Results:
None of the plates showed any growth.

===June 3/2010===

@@ Line 228: / Line 228: @@
 <b>Objective:</b> Ligate pBad-TetR part with fluorescent protein part in pSB1C3 backbone.<br>
+<b>Method:</b><br>
+<u>Restriction</u><br>
+<table><table border ="3">
+<tr><td><b>Name</b></td><td><b>Volume<br>pDNA (&micro;L)</b></td><td><b>Volume<br>Water (&micro;L)</b></td><td><b>Volume<br>Buffer (&micro;L)</b></td><td><b>Enzymes</b></td><td><b>Total Volume</b></td></tr>
+<tr><td>pSB-NEYFP (B4)</td><td>.8</td><td>43.7</td><td>5</td><td>0.25&micro;L XbaI<br>0.25&micro;L PstI</td><td>50</td></tr>
+<tr><td>pSB-CEYFP (B5)</td><td>.9</td><td>43.6</td><td>5</td><td>0.25&micro;L XbaI<br>0.25&micro;L PstI</td><td>50</td></tr>
+<tr><td>pBad-TetR)</td><td>.3</td><td>44.2</td><td>5</td><td>0.25&micro;L EcoRI<br>0.25&micro;L SpeI</td><td>50</td></tr>
+<tr><td>NEYFP (E1)</td><td>4.3</td><td>40.7</td><td>5</td><td>0.25&micro;L XbaI<br>0.25&micro;L PstI</td><td>50</td></tr>
+<tr><td>NEYFP (E2)</td><td>0.3</td><td>42.2</td><td>5</td><td>0.25&micro;L XbaI<br>0.25&micro;L PstI</td><td>50</td></tr>
+<tr><td>Fusion CEYFP (E3)</td><td>3.9</td><td>40.6</td><td>5</td><td>0.25&micro;L XbaI<br>0.25&micro;L PstI</td><td>50</td></tr>
+<tr><td>Fusion CEYFP (E4)</td><td>2.0</td><td>42.5</td><td>5</td><td>0.25&micro;L XbaI<br>0.25&micro;L PstI</td><td>50</td></tr>
+<tr><td>Fusion CEYFP (E5)</td><td>3.0</td><td>41.5</td><td>5</td><td>0.25&micro;L XbaI<br>0.25&micro;L PstI</td><td>50</td></tr>
+<tr><td>CEYFP (E6)</td><td>0.6</td><td>43.9</td><td>5</td><td>0.25&micro;L XbaI<br>0.25&micro;L PstI</td><td>50</td></tr>
+<tr><td>CEYFP (E7)</td><td>0.5</td><td>44.0</td><td>5</td><td>0.25&micro;L XbaI<br>0.25&micro;L PstI</td><td>50</td></tr>
+<tr><td>pBad-TetR (F4)</td><td>2.5</td><td>42</td><td>5</td><td>0.25&micro;L EcoRI<br>0.25&micro;L SpeI</td><td>50</td></tr>
+<tr><td>pBad-TetR (F5)</td><td>1.7</td><td>42.8</td><td>5</td><td>0.25&micro;L EcoRI<br>0.25&micro;L SpeI</td><td>50</td></tr>
+<tr><td>pSB-CEYFP (G4)</td><td>2.9</td><td>41.6</td><td>5</td><td>0.25&micro;L XbaI<br>0.25&micro;L PstI</td><td>50</td></tr>
+<tr><td>pSB1C3</td><td>15.5</td><td>46</td><td></td><td>0.25&micro;L EcoRI<br>0.25&micro;L PstI</td><td>62</td></tr></table>
+Incubated at 37<sup>o</sup>C for 75 minutes.<br>
+*Used Red buffer for the EcoRI/SpeI and EcoRI/PstI digests
+*Used Tango buffer for the XbaI/PstI digests
+*Did not heat kill upon removal from incubation, put directly into -20<sup>o</sup>C fridge.
+<b>Continue Ligation on Saturday (See below).</b><br>
+===June 5/2010 ===
+(In the lab:AS)<br>
+<b>Objective:</b> Ligate restriction products from June 3/2010.<br>
+<b>Relevant information:</b> <br>
+*Have 3 tubes of part 1 (pBad-TetR)
+**In ampicillin backbone
+*Have 10 tubes of part 2 (fluorescent protein - various)
+**In ampicillin backbone
+*Will have 30 combinations
+*Will use pSB1C3 as plasmid backbone
+**Used most of the pSB1T3 and want to save remainder for creating new backbone via PCR.
+<b>Method:</b><br>
+<b>*Restriction digests were not heat killed after reactions. Freezing probably killed the restriction enzymes, but I will hea kill them at 80<sup>o</sup>C for 20 minutes anyways prior to adding Ligase.</b>
+**Cool on ice for 10 minutes before adding ligase.
+<table><table border ="3">
+<tr><td><b>Master Mix</b></td><td><b>Volume/tube (&micro;L)</b></td><td><b>Total Volume (&micro;L)</b></td></tr>
+<tr><td>DNA</td><td>6</td><td>---</td></tr>
+<tr><td>10x Buffer</td><td>1</td><td>32</td></tr>
+<tr><td>T4 DNA Ligase</td><td>.25</td><td>8</td></tr>
+<tr><td>MilliQ H<sub>2</sub>O</td><td>2.75</td><td>88</td></tr></table>
+*Add 4&micro;L master mix to each DNA tube.<br>
+<b>Follow-up:</b> Ligation reactions will be transformed into DH5&alpha; cells<br>
 ===June 6/2010 ===

Component	Volume (µL)
MilliQ H₂O	15.5
Buffer	2
pDNA	2
Enzyme	0.25 + 0.25