Team:Lethbridge/Notebook/Lab Work/June

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Latest revision as of 01:36, 25 October 2010

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Here you can check out the work we have done in the lab, click on a month to take a look!

Contents

1 June 2010

1.1 June 1/2010

1.2 June 2/2010

1.3 June 2/2010 - Evening

1.4 June 3/2010

1.5 June 3/2010 - Evening

1.6 June 5/2010

1.7 June 6/2010

1.8 June 7/2010

1.9 June 7/2010 - Evening

1.10 June 8/2010

1.11 June 8/2010 - Evening

1.12 June 9/2010

1.13 June 10/2010

1.14 June 14/2010 Evening

1.15 June 15/2010

1.16 June 15/2010 Evening

1.17 June 16/2010

1.18 June 16/2010 Evening

1.19 June 17/2010

1.20 June 17/2010 Evening

1.21 June 18/2010

1.22 June 21/2010

1.23 June 22/2010

1.24 June 22/2010 Evening

1.25 June 23/2010

1.26 June 24/2010

1.27 June 28/2010

1.28 June 30/2010

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 7/2010

(In Lab: JV, HB, TF, AV)

Objective:
Purification of DNA to increase ligation and transformation efficiency.

Method:
BioBasic Protocol for Purification of PCR products.

DNA (from Working Plasmid Box) Purified:

pBAD-TetR (B10)
pBAD- TetR (F4)
pBAD-TetR (F5)
EYFP (B1)
pSB-NEYFP (B4)
pSB-CEYFP (B5)
NEYFP (E1)
NEYFP (E2)
Fusion CEYFP (E3)
Fusion CEYFP (E4)
Fusion CEYFP (E5)
CEYFP (E6)
CEYFP (E7)
EYFP (E8)
EYFP (E9)
EYFP (E10)
ECFP (F1)
ECFP (F2)
ECFP (F3)
EYFP (G1)
pSB-CEYFP (G4)

Objective:
Restrict and run 1% agarose gel of plasmids J5, J6, and pSB1T3 (June 2/10).

Method:
Restrictions

Component Volume (µL)

Restriction Enzyme (XbaI) 0.25

Buffer (Tango) 2

Plasmid DNA 2

MilliQ H₂O 15.75

Incubated for 1 hour in 37^oC incubator.
Heat shocked for 10 min at 65^oC on heating block.

1% Agarose Gel

Lane Sample Load (µL)

1 1kb ladder 2 ladder + 2 dye (6X) + 8 MilliQ H₂O

2 J5-pLacI-SRBS-Lumazine-dT(1) 10 DNA + 2 Dye (6X)

3 J5-pLacI-SRBS-Lumazine-dT(1)restricted 10 DNA + 2 Dye (6X)

4 J6-pLacI-SRBS-Lumazine-dT(2) 10 DNA + 2 Dye (6X)

5 J5-pLacI-SRBS-Lumazine-dT(2)restricted 10 DNA + 2 Dye (6X)

6 pSB1T3 10 DNA + 2 Dye (6X)

7 pSB1T3 restricted 10 DNA + 2 Dye (6X)

8 Empty

9 Empty

10 Empty

Ran at 100V for 72 min.

IMAGE TO COME!!!!!!

June 7/2010 - Evening

(In Lab: AS, KG)

Objective:
Ligation of:

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

Method:
FILL ME IN!!!!!!

June 8/2010

(In the lab: JV, AV)
Objective: Follow the overexpression of our pLacI-sRBS-Lum-dT construct.
Method: FILL ME OUT!!!!!!
Results:

Time OD₆₀₀ F1 OD₆₀₀ E10

0 0.118 0.103

30 0.133 0.111

30 0.145 0.116

90

120 0.160 0.124

150 0.120 0.093

180 0.129 0.100

210 0.145 0.122

240 0.158 0.145

270 0.171 0.178

300 0.194 0.222

330 0.223 0.280

360 0.252 0.364

390 0.296 0.458

420 0.338 0.557^†

450 0.394 0.656

480 0.453 0.675

510 0.530 0.688

540 0.598^† 0.706

600 0.633 0.752

660 0.653

720 0.679

∞ 1.278

† Overexpression induced by adding 1mM IPTG.
Following overexpression, 1mL of cells was removed from the culture, spun down at ~13000xg for 20 seconds, excess media removed and rinsed with water.
Suspended cells in 8M urea, mixed with 6x dye and ran on 18% SDS-PAGE gel for 90 minutes at 200V. Gel stained overnight.
Results: IMAGE TO COME!!!!

Objective: Calculate quantity of DNA in pBad-TetR and fluorescent protein mini-preps by staining an agarose gel.
Method: Restrict plasmid DNA (done by AV,HB,TF on June 7/2010) and run on a 1% TAE agarose gel (JV).

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
EYFP (B1) 10µL DNA
2µL Dye Restricted
Fusion CEYFP (E3) 10µL DNA
2µL Dye

3 Unrestricted
EYFP (B1) 10µL DNA
2µL Dye Unrestricted
Fusion CEYFP (E3) 10µL DNA
2µL Dye

4 Restricted
pSB-CEYFP (B5) 10µL DNA
2µL Dye Restricted
Fusion CEYFP (E4) 10µL DNA
2µL Dye

5 Unrestricted
pSB-CEYFP (B5) 10µL DNA
2µL Dye Unrestricted
Fusion CEYFP (E4) 10µL DNA
2µL Dye

6 Restricted
ECFP (F2) 10µL DNA
2µL Dye Restricted
EYFP (E10) 10µL DNA
2µL Dye

7 Unrestricted
ECFP (F2) 10µL DNA
2µL Dye Unrestricted
EYFP (E10) 10µL DNA
2µL Dye

8 Restricted
pSB-CEYFP (G4) 10µL DNA
2µL Dye Restricted
pSB NEYFP (B4) 10µL DNA
2µL Dye

9 Unrestricted
pSB-CEYFP (G4) 10µL DNA
2µL Dye Unrestricted
pSB NEYFP (B4) 10µL DNA
2µL Dye

10 Restricted
EYFP (G1) 10µL DNA
2µL Dye Restricted
ECFP (F3) 10µL DNA
2µL Dye

11 Unrestricted
EYFP (G1) 10µL DNA
2µL Dye Unrestricted
ECFP (F3) 10µL DNA
2µL Dye

12 Restricted
NEYFP (E2) 10µL DNA
2µL Dye pBad-TetR (F5) 10µL DNA
2µL Dye

13 Unrestricted
NEYFP (E2) 10µL DNA
2µL Dye Restricted
Fusion CEYFP (E5) 10µL DNA
2µL Dye

14 Restricted
pBad-TetR (B10) 10µL DNA
2µL Dye Unrestricted
Fusion CEYFP (E5) 10µL DNA
2µL Dye

15 Unrestricted
pBad-TetR (B10) 10µL DNA
2µL Dye pBad-TetR (F4) 10µL DNA
2µL Dye

16 Restricted
CEYFP (E6) 10µL DNA
2µL Dye Restricted
pSB1T3 10µL DNA
2µL Dye

17 Unrestricted
CEYFP (E6) 10µL DNA
2µL Dye Unrestricted pSB1T3 10µL DNA
2µL Dye

18 Restricted
NEYFP (E1) 10µL DNA
2µL Dye 10µL DNA
2µL Dye

19 Unrestricted
NEYFP (E1) 10µL DNA
2µL Dye

20 Restricted
ECFP (F1) 10µL DNA
2µL Dye

21 Unrestricted
ECFP (F1) 10µL DNA
2µL Dye

22 Restricted
EYFP (E9) 10µL DNA
2µL Dye

23 Unrestricted
EYFP (E9) 10µL DNA
2µL Dye

24 Restricted
CEYFP (E7) 10µL DNA
2µL Dye

25 Unrestricted
CEYFP (E7) 10µL DNA
2µL Dye

26 Restricted
EYFP (E8) 10µL DNA
2µL Dye

27 Unrestricted
EYFP (E8) 10µL DNA
2µL Dye

Ran gel at 100V for 90 minutes.
Results:

No bands visible except for pSB1T3 lanes, therefore could not quantify anything that had not already been quantified.
Also, purification of DNA done on June 7/2010 seemed to reduce amount of pDNA in sample.

Objective: Restrict mms6 (D9,D10) and dT (C1) so we can ligate the dT onto the mms6 coding region.
Method:
mms6 Restriction

2µL mms6 pDNA
2µL Red buffer
0.25µL EcoRI
0.25µL SpeI
15.5µL MilliQ H₂O

dT Restriction

2µL dT pDNA
2µL Orange buffer
0.25µL EcoRI
0.25µL XbaI
15.5µL MilliQ H₂O

Incubated for 1 hour at 37^oC
Heat shock on heat block (80^oC) for 20 minutes
Ligation

2µL dT pDNA
2µL mms6 pDNA
0.25µL T4 DNA Ligase
1µL 10x buffer
4.75µL MilliQ H₂O

Analyze results on 1% TAE agarose gel

Lane Sample Load (µL)

1 1kb ladder 0.5 ladder; 2 dye; 9.5 MilliQ H₂O

2 Unrestricted mms6 (D9) 10 DNA; 2 Dye

3 Restricted mms6 (D9) 10 DNA; 2 Dye

4 Unrestricted mms6 (D10) 10 DNA; 2 Dye

5 Restricted mms6 (D10) 10 DNA; 2 Dye

6 Unrestricted dT (C1) 10 DNA; 2 Dye

7 Restricted dT (C1) 10 DNA; 2 Dye

8 Empty

9 Empty

10 Empty

Results:

Looks like the mms6 DNA was not cut at all. Therefore is doubtful that the ligations will work.

June 8/2010 - Evening

Objective: Transform pLacI-sRBS-Lum-dT constructs assembled via three antibiotic assembly on June 3/2010. Also transform mms6-dT constructs assembled today using old insertion method.
Method: Follow transformation protocol. Results: No colonies anywhere

June 9/2010

(in the lab: TF, JV)
Objective: Transform mms6-dT ligation reactions from June 8/2010.
Method: Followed transformation protocol and transformed the following:

mms6 (D9) + dT (C1)
mms6 (D10) + dT (C1)
pUC19 (positive control)
Water (negative control)

Results: No transformants on plates.

June 10/2010

(In the lab: AV, HB, JV)
Objective: Repeat ligation of mms6 (B9,D9,D10) and dT (C1).
Method:
mms6 Restriction

2µL mms6 pDNA
2µL Red buffer
0.25µL EcoRI
0.25µL SpeI
15.5µL MilliQ H₂O

dT Restriction

2µL dT pDNA
2µL Orange buffer
0.25µL EcoRI
0.25µL XbaI
15.5µL MilliQ H₂O

Incubated for 1 hour at 37^oC.
Killed enzymes by heating to 80^oC for 20 minutes
Ligation

5µL dT pDNA
5µL mms6 pDNA
0.5µL T4 DNA Ligase
2µL 10x buffer
7.5µL MilliQ H₂O

Incubated at room temperature overnight.
Results:
Analyzed on 1% TAE agarose gel:

Lane Sample Load (µL)

1 1kb ladder 0.5 ladder; 2 dye; 9.5 MilliQ H₂O

2 Unrestricted mms6 (B9) 5 DNA; 2 dye; 5 MilliQ H₂O

3 Restricted mms6 (B9) 5 DNA; 2 dye; 5 MilliQ H₂O

4 Unrestricted mms6 (D9) 5 DNA; 2 dye; 5 MilliQ H₂O

5 Restricted mms6 (D9) 5 DNA; 2 dye; 5 MilliQ H₂O

6 Unrestricted mms6 (D10) 5 DNA; 2 dye; 5 MilliQ H₂O

7 Restricted mms6 (D10) 5 DNA; 2 dye; 5 MilliQ H₂O

8 Unrestricted dT (C1) 5 DNA; 2 dye; 5 MilliQ H₂O

9 Restricted dT (C1) 5 DNA; 2 dye; 5 MilliQ H₂O

10 D9 + C1 Ligation (June 8/2010) 5 DNA; 2 dye; 5 MilliQ H₂O

Gel run for 80 minutes at 100V

Looks like everything was restricted. Ligations may work this time.
Follow-up: Ligation mixtures can be restriction tested and (if cutting works) transformed into DH5α cells.

Objective: Transform pDNA from distribution plates into DH5α cells to generate glycerol stocks for lab.
Method:
Remove DNA from the following locations on the 2010 distributions kits:

double terminator (B0010-B0010; AKA B0017) from kit plate 2 well 6K (pSB1A2)
double terminator (B0010-B0012; AKA B0015) from kit plate 1 well 23L (pSB1AK3)

Transform into DH5α cells using transformation protocol, with pUC19 as positive control (1ng/µL), and water as negative control.
Results:

Positive control: TMTC (too many to count) colonies
B0010-B0010: 41 colonies
B0010-B0012: 120 colonies

June 14/2010 Evening

(In the lab: TF, DM, HS)
Objective: Restriction Digest of RBS-xylE with EcoRI and SpeI

Method:

Restriction Digestions

Pipetted 15.5µL of water, into 2 reaction tubes (0.6mL) each.
Pipetted 2µL of red buffer into each of them.
Pipetted 2µL of rbs-xylE plasmid DNA into both tubes, but taking only the thawed liquid on the side.
Because this was not proper protocol for aliquoting DNA, we thawed the DNA out completely and then put 2µL more of the rbs-xylE plasmid DNA in.
Pipetted 0.25µL of EcoRI enzyme and 0.25µL of SpeI enzyme into the restriction reaction tube.
Placed in incubator (37^oC) for 1 hour.
Placed in ice for 10 minutes.

Objective: Test Ligations of rbs-xylE with T4-Ligase from iGEM -20^oC and from HJ's lab's -20^oC.

Method:

Pipette 12.75µL of Milli-Q H₂O into 4 mincrocentrifuge tubes.
Pipette 2µL of 10X T4-Ligase buffer into all 4 tubes.
Pipette 5µL of the RD product into both iGEM ligase tubes and HJ-Lab Ligase tubes.
Pipetted 5µL of the RD control into both iGEM ligase tubes and HJ-Lab ligase tubes.
Incubate overnight

June 15/2010

(In the lab: JV)

Objective:Continue T4-Ligase check and confirm that it is functional.

Method:Run plasmid DNA;uncut, cut, and ligated on a 1% agarose gel (TAE)

Lane Sample Load (µL)

1 rbs-xylE 10 DNA solution + 2 Dye

2 rbs-xylE R.D. 10 DNA solution + 2 Dye₂O

3 rbs-xylE [iGEM ligation] 10 DNA solution + 2 Dye

4 rbs-xylE [HJ ligation] 10 DNA solution + 2 Dye

5 rbs-xylE [iGEM ligation control] 10 DNA solution + 2 Dye

6 rbs-xylE [HJ ligation control] 10 DNA solution + 2 Dye

7 1kb ladder 2 ladder + 2 dye + 8 Milli-Q H₂O

8 mms6 (B9) R.D. 10 DNA solution + 2 Dye

9 mms6 (B9) 10 DNA solution + 2 Dye

10 mms6 (D10) R.D. 10 DNA solution + 2 Dye

11 mms6 (D10) 10 DNA solution + 2 Dye

12 mms6 (D9) R.D. 10 DNA solution + 2 Dye

13 mms6 (D19) 10 DNA solution + 2 Dye

14 dt (C1) R.D. 10 DNA solution + 2 Dye

15 dt (C1) 10 DNA solution + 2 Dye

Result:Ran gel for 89 minutes at 100V. Gel was unreadable. I will redo the gel using and 8 well comb. IMAGE TO COME!!!!

Lane Sample Load (µL)

1 rbs-xylE R.D. 5 DNA solution + 1 Dye

2 rbs-xylE 5 DNA solution + 1 Dye

3 iGEM ligation 10 DNA solution + 2 Dye

4 iGEM ligation control 10 DNA solution + 2 Dye

5 HJ ligation 10 DNA solution + 2 Dye

6 HJ ligation control 10 DNA solution + 2 Dye

7 1kb ladder 2 ladder + 2 dye + 8 Milli-Q H₂O

Ran gel at 100V for 82 minutes.

Result:The gel "broke" while running. Jeff hypothesized the cause to be excessive heat. However, the DNA was still visible.IMAGE TO COME!!!!

Objective:Isolate plasmid DNA from DH5α cells.

Method:The plasmid DNA is:

1)double terminator B0017 (B0010-B0010) from 2010 kit plate 2:6K pSB1A2
2)double terminator B0015 (B0010-B0012) from 2010 kit plate 1:23L pSB1AK2

This will give us 2 additional dt's (3 total) into our working plasmid box to ligate onto the end of our constructs.

Used the boiling lysis miniprep protocol and elute with 50µL of Milli-Q H₂O with RNAse A.

These plasmids (labeled 1 & 2 above) are in:

working plasmid box: 1). J9 2). J10

glycerol sotck 2010 box: 1). F2 2). F3

DNA was then purified using the protocol for purification of PCR products (BioBasic). DNA was eluted with 35µL of elution buffer.

June 15/2010 Evening

(In the lab: AS)

Adam: not convinced that the rbs-xylE was cut properly last night. There doesn't appear to be and band where the insert should be.

Objective: To confirm that EcoRI & SpeI are cutting (also PstI). Use rbs-xylE as test plasmid DNA.

Method: Digest rbs-xylE with the following enzyme combinations:

EcoRI + SpeI (old [i.e. John's]) + Red Buffer
EcoRI + SpeI (new) + Red Buffer
EcoRI + PstI + Red Buffer
EcoRi + Red Buffer
SpeI (old) + Tango Buffer
SpeI (new) + Tango Buffer
PstI + Red Buffer
No enzyme controls (Red & Tango Buffer)

Reaction mix as follows:

Milli-Q H₂O 15.5µL
10X Buffer 2µL
pDNA 2µL
Enzymes 0.25µL + 0.25µL

Incubated at 37^oC for 1 hour . Analyze on 1% TAE Agarose gel as follows:

Lane Sample Load (µL)

1 No Enzyme Control (Tango) 10 DNA solution + 2 Dye

2 No Enzyme Control (Red) 10 DNA solution + 2 Dye

3 PstI 10 DNA solution + 2 Dye

4 SpeI (old) 10 DNA solution + 2 Dye

5 SpeI (new) 10 DNA solution + 2 Dye

6 EcoRI 10 DNA solution + 2 Dye

7 EcoRI + SpeI (old) 10 DNA solution + 2 Dye

8 EcoRI + SpeI (new) 10 DNA solution + 2 Dye

9 EcoRI + PstI 10 DNA solution + 2 Dye

10 1kb ladder 0.5 ladder + 2 dye + 9.5 Milli-Q H₂Oe

Results: Everything cuts exactly as it should. Continue with ligation and analysis. IMAGE TO COME!!!!

June 16/2010

(in lab: JV) Objective: To miniprep Adam's overnight cultures of xylE and rbs. Completing this will give us a working stock of this plasmid.

Method: Use the boiling lysis miniprep protocol and pufrify using BioBasic protocol for purification of PCR products.

Objective: Transform pLacI-sRBS-lumazine synthase-dt into BL21(DE3).

Method:

Followed transformation protocol

Changes to the protocol include:

Added 5µL DNA to 50µL BL21(DE3).
Incubated in 500µL SOC instead of 250µL LB
incubated for 90 minutes at 37^oC at 4:30pm.

Results: There wasn't any growth after overnight incubation. Possibility of an antibiotic mix-up.

June 16/2010 Evening

(in lab: ADS)
Objective: Continue with ligation test. Use restriction products to test T4 DNA ligase.

Method: Have 10µL of DNA remaining for each restriction. Ligate together one of the single cut reactions, and ligate one of the double cut reactions. 4µL of each sample will be tested against each ligase.
i.e.

EcoRI +SpeI (new) cut vs HJ's ligase
EcoRI + SpeI (new) cut vs iGEM ligase
SpeI (new) cut vs HJ's ligase
SpeI (new) cut vs iGEM ligase

Reaction Mixture:

DNA -> 4µL
10X Buffer -> 2µL
Milli-Q -> 13.5µL
Ligase -> 0.5µL

Prior to setting up reaction, heat kill restriction enzymes by heating to 80^oC for 20 minutes and subsequently cooling on ice for 10 minutes.

Ligations begun at 6:50pm

Will run samples at 30 minutes reaction time and overnight.

Analyze ligations in a 1% TAE Agarose gel

Lane Sample Load (µL)

1 No Enzyme Control (from last night) 1 DNA solution + 1 Dye + 4 H₂O

2 EcoRI + SpeI (old)(from last night) 1 DNA solution + 1 Dye + 4 H₂O

3 EcoRI + SpeI (new) vs HJ's Ligase 5 DNA solution + 1 Dye

4 EcoRI + SpeI (new) vs iGEM ligase 5 DNA solution + 1 Dye

5 SpeI (new) vs HJ's Ligase 5 DNA solution + 1 Dye

6 SpeI (new) vs iGEM ligase 5 DNA solution + 1 Dye

7 SpeI (old)(from last night) 1 DNA solution + 1 Dye + 4 H₂O

8 1kb Ladder 0.25 Ladder + 4.75 H₂O + 1 Dye

No observable ligation occurring 30 minutes with both ligases.

Objective: Prepare DNA for sequencing

Method: Need 20µL of DNA at 100ng/µL for each reaction. Need 20µL of 10µM primer for every 5 reactions.

Plasmids that need to be sequenced:

Name Concentration (ng/µL) Dilution Factor Final Concentration (ng/µL)

A8-CFP complete 1395 1/5 280

B4-pSB NEYFP 1105 1/5 240

B5-pSB CEYFP 1055 1/5 210

B6-CFP complete 1285 1/5 260

D7-xylE 1820 1/10 182

D8-xylE 420 1/2 210

E1-NEYFP 235 1/2 117.5

E2-NEYFP 2980 1/10 300

E3-Fusion CEYFP 255 1/2 122.5

E4-Fusion CEYFP 490 1/2 245

E5-Fusion CEYFP 335 1/2 335

E6-CEYFP 1605 1/10 160

E7-CEYFP 1930 1/10 190

G4-pSB CEYFP 340 1/4 85

G5-CFP complete 355 1.4 89

Total of 15 primers -> 30 reactions
60µL of each VF2 & VR primers (10µL) -> send 65µL

June 17/2010

(in lab: JV, HB) Objective:Run Agarose gel of overnight samples from June 16/10 to test T4 DNA ligase

Method:Analyze ligation on a 1% TAE agarose gel.

Lane Sample Load (µL)

1 No Enzyme Control (from June 15) 2 DNA solution + 2 Dye + 8 H₂O

2 EcoRI + SpeI (old)(from June 15) 2 DNA solution + 2 Dye + 8 H₂O

3 EcoRI + SpeI (new) vs HJ's Ligase 10 DNA solution + 2 Dye

4 EcoRI + SpeI (new) vs iGEM ligase 10 DNA solution + 2 Dye

5 SpeI (new) vs HJ's Ligase 10 DNA solution + 2 Dye

6 SpeI (new) vs iGEM ligase 10 DNA solution + 2 Dye

7 SpeI (old)(from last night) 10 DNA solution + 2 Dye

8 1kb Ladder 0.5 Ladder + 9.5 H₂O + 2 Dye

Ran for 80 minutes at 100V.
Results:
IMAGE TO COME!!!!

June 17/2010 Evening

(in lab: JS, AS, KG)

Objective:Do PCR to observe ligations

Method:

Master Mix Volume/tube (µL) Total Volume (µL)

MilliQ H₂O 10.8 59.4

DNA 2 -------

5X Phusion Buffer 4 22

10µM dNTP's .25 8

Forward Primer 1 5.5

Reverse Primer 1 5.5

Polymerase 0.2 1.1

Reaction Mixtures:

HJ Double
iGEM Double
HJ Single
iGEM Single
controls (no forward or reverse primer and no DNA)

June 18/2010

(in lab: JV)

Objective:Observe the ligations from June 17/10 that were amplified using PCR.

Method:Observe using 1% TAE agarose gel electrophoresis. Ran the gel for 80 minutes at 100V.

Lane Sample Volume (µL)

8 1kb Ladder 2 Ladder + 8 H₂O + 2 Dye

2 control no DNA 20 PCR reaction + 4 6X Dye and used 12 of this solution

3 control no reverse primer 20 PCR reaction + 4 6X Dye and used 12 of this solution

4 control no forward primer 20 PCR reaction + 4 6X Dye and used 12 of this solution

5 HJ single 20 PCR reaction + 4 6X Dye and used 12 of this solution

6 iGEM single 20 PCR reaction + 4 6X Dye and used 12 of this solution

7 HJ double 20 PCR reaction + 4 6X Dye and used 12 of this solution

8 HJ double 20 PCR reaction + 4 6X Dye and used 12 of this solution

Results:IMAGE TO COME!!!!

June 21/2010

(in lab: JV)

Objective:Create more pSB1A3 plasmid.

Method:Run a PCR of the plasmid.

DIlute 10X -> 0.1 + 0.9 MilliQ H₂O DIlute 10X -> 0.1 + 0.9 MilliQ H₂O

Master Mix Volume/tube (µL)

MilliQ H₂O 10.8

DNA 2
5X Phusion Buffer 4
10µM dNTP's .25
Forward Primer 1
Reverse Primer 1
Polymerase 0.2

Use ligtest setting. WIll run 36 cycles.
Use 3 controls:

no forward primer
no reverse primer
no DNA

Results:PCR samples were run on a gel (1% 1XTAE) with the PCR samples from June 22/10. This gel was run on June 22/10

June 22/2010

(in lab: JV, HS)

Objective:To overexpress pLacI-sRBS-lumazine synthase-dt in DH5α cells.

Method:Incubate cells in 500mL LB w/Tet. At OD 0.6 (600λ) induce overexpression of lumazine synthase with IPTG (1µM). Take T_o, T₁, T₂, T₃ readings after induced with IPTG.

Time OD F1 (600λ) OD E10 (600λ)

0 0.078 0.072

60 0.122 0.110

90 0.128 0.125

120 0.140 0.138

150 0.149 0.157

180 0.169 0.183

210 0.205 0.230

240 0.243 0.276

270 0.278 0.323

300 0.317 0.398

330 0.394 0.428

360 0.394 0.480

390 0.441 0.553

400 ---- 0.594 (induced)

410 0.502 -----

450 0.580 (induced) 0.736

510 0.804 1.005

570 1.065 1.066

630 1.053 1.043

∞ 0.055 (1/10 dilution) 0.078 (1/10 dilution)

Objective:PCR amplify the following biobricks:

dt (23L)
dt (6K)
dt (C1)
mms6
control (no DNA)

Method:

Master Mix Volume/tube (µL) Total Volume (µL)

MilliQ H₂O ---- 89.6

DNA 2 -------

5X Phusion Buffer 4 24

10µM dNTP's .4 2.4

Forward Primer 0.2 1.2

Reverse Primer 0.2 1.2

Polymerase 0.2 1.2

1.2% Agarose gel electrophoresis (1X TAE), used to analyze the above PCR's. 25mL of agarose solution was used in the small gel rig.

Lane Sample Volume (µL)

1 pSB1A3 1 PCR sample + 2 Dye + 9 H₂O

2 no DNA 1 PCR sample + 2 Dye + 9 H₂O

3 no reverse primer 1 PCR sample + 2 Dye + 9 H₂O

4 no forward primer 1 PCR sample + 2 Dye + 9 H₂O

5 1kb ladder 0.5 ladder + 2 dye + 9.5 Milli-Q H₂O

6 mms6 1 PCR sample + 2 Dye + 9 H₂O

7 dt (23L) 1 PCR sample + 2 Dye + 9 H₂O

8 dt (6K) 1 PCR sample + 2 Dye + 9 H₂O

9 dt (C1) 1 PCR sample + 2 Dye + 9 H₂O

10 no DNA 1 PCR sample + 2 Dye + 9 H₂O

Ran the gel for 40 minutes at 100V.

June 22/2010 Evening

(in lab: KG, AS)

Objective:To run a PCR of:

dt (J9,J10,C1)
mms6 (B9,F10)
rbs-xylE (I1,I2)
xylE (D7, D8)
pLacI-sRBS-lumazine synthase-dt (I8,I9)
sRBS-lumazine synthase-dt (A1,A2,B7,B8,G2,G3)
pLacI (A9,D1)
pSB1A3

so that we have more DNA for restrictions and ligations.

Method:

Master Mix 1 Volume/tube (µL) Total Volume (µL)

MilliQ H₂O 10.8 226.8

DNA 2 4

5X Phusion HF Buffer 4 84

10µM dNTP's 1 21

Forward Primer (VF2) 1 21

Reverse Primer (VR) 1 21

Fimnzzymes polymerase 0.2 4.2

Master Mix 2 Volume/tube (µL) Total Volume (µL)

MilliQ H₂O 10.8 226.8

DNA 2 4

5X Econo Taq Buffer 4 84

10µM dNTP's 1 21

Forward Primer (VF2) 1 21

Reverse Primer (VR) 1 21

Imitrages polymerase (Econo Taq) 0.2 4.2

Master Mix for pSB1A3 Volume/tube (µL) Total Volume (µL)

MilliQ H₂O 10.8 31

DNA 1 20

5X Phusion Buffer 4 10

10µM dNTP's 1 2.5

Primer (SB-prep-2Ea) 1 2.5

Primer (SB-prep-3P) 1 2.5

Fimnzzymes polymerase 0.2 0.5

Master Mix for pSB1A3 Volume/tube (µL)

MilliQ H₂O 10.8

DNA 2

5X Econo Taq Buffer 4

10µM dNTP's 1

Primer (SB-prep-2Ea) 1

Primer (SB-prep-3P) 1

Imitrages polymerase 0.2

June 23/2010

(in lab: JV, HS)

Objective:: To run the pcr products on an agarose gel.

Method: Run on 1% agarose gel using the large gel rig.

Lane Sample Load (µL)

1 1kb DNA Ladder 0.5 Ladder + 2 Dye + 9 H₂O

2 Phu-dt-J9 5 PCR sample + 2 Dye + 3 H₂O

3 Phu-dt-J10 5 PCR sample + 2 Dye + 3 H₂O

4 Phu-dt-C1 5 PCR sample + 2 Dye + 3 H₂O

5 Fus-mms6-B9 5 PCR sample + 2 Dye + 3 H₂O

6 Fus-mms6-F10 5 PCR sample + 2 Dye + 3 H₂O

7 Fus-rbs-xylE-I1 5 PCR sample + 2 Dye + 3 H₂O

8 Fus-rbs-xylE-I2 5 PCR sample + 2 Dye + 3 H₂O

9 Fus-xylE-D7 5 PCR sample + 2 Dye + 3 H₂O

10 Fus-xylE-D8 5 PCR sample + 2 Dye + 3 H₂O

11 Fus-pLacI-sRBS-lum-dt I8 5 PCR sample + 2 Dye + 3 H₂O

12 Fus-pLacI-sRBS-lum-dt I9 5 PCR sample + 2 Dye + 3 H₂O

13 Fus-sRBS-lum-dt A1 5 PCR sample + 2 Dye + 3 H₂O

14 Phu-sRBS-lum-dt A2 5 PCR sample + 2 Dye + 3 H₂O

15 Phu-sRBS-lum-dt B7 5 PCR sample + 2 Dye + 3 H₂O

16 Phu-sRBS-lum-dt B8 5 PCR sample + 2 Dye + 3 H₂O

17 Phu-sRBS-lum-dt G2 5 PCR sample + 2 Dye + 3 H₂O

18 Phu-sRBS-lum-dt G3 5 PCR sample + 2 Dye + 3 H₂O

19 Phu-pLacI A9 5 PCR sample + 2 Dye + 3 H₂O

20 Phu-pLacI D1 5 PCR sample + 2 Dye + 3 H₂O

21 dt J9 5 PCR sample + 2 Dye + 3 H₂O

22 dt J10 5 PCR sample + 2 Dye + 3 H₂O

23 dt C1 5 PCR sample + 2 Dye + 3 H₂O

24 mms6 B9 5 PCR sample + 2 Dye + 3 H₂O

25 mms6 F10 5 PCR sample + 2 Dye + 3 H₂O

26 rbs-xylE I1 5 PCR sample + 2 Dye + 3 H₂O

27 rbs-xylE I2 5 PCR sample + 2 Dye + 3 H₂O

28 xylE D7 5 PCR sample + 2 Dye + 3 H₂O

29 xylE D8 5 PCR sample + 2 Dye + 3 H₂O

30 pLacI-sRBS-lum-dt I8 5 PCR sample + 2 Dye + 3 H₂O

31 pLacI-sRBS-lum-dt I9 5 PCR sample + 2 Dye + 3 H₂O

32 sRBS-lum-dt A1 1 PCR sample + 2 Dye + 9 H₂O

33 sRBS-lum-dt A2 1 PCR sample + 2 Dye + 9 H₂O

34 sRBS-lum-dt B7 1 PCR sample + 2 Dye + 9 H₂O

35 sRBS-lum-dt B8 1 PCR sample + 2 Dye + 9 H₂O

36 sRBS-lum-dt G2 1 PCR sample + 2 Dye + 9 H₂O

37 sRBS-lum-dt G3 1 PCR sample + 2 Dye + 9 H₂O

38 sRBS-lum-dt A9 1 PCR sample + 2 Dye + 9 H₂O

39 sRBS-lum-dt D1 0.5 ladder + 2 dye + 9.5 Milli-Q H₂O

40 pSB1A3 control 5 PCR sample + 2 Dye + 3 H₂O

41 pSB1A3 5 PCR sample + 2 Dye + 3 H₂O

42 pSB1A3 control 5 PCR sample + 2 Dye + 3 H₂O

43 pSB1A3 5 PCR sample + 2 Dye + 3 H₂O

Ran gel for 45 minutes at 100V and stained in EtBr for 20 minutes and de-stained for 10 minutes.

all Econe tubes are red
all Phusion tubes are blue

Results: IMAGE!!!

Objective: Adam put in overnight cultures on June 22. I want to extract the plasmid DNA.

Method:

Put in overnight cultures at 8:30pm and taken out at 9:30am next morning.
All cultures were DH5α in LB w/ Amp.
Cultures were incubated at 37_oC.
Next morning cultures were "minipreped" using boiling lysis miniprep protocol.

Results: Will view plasmid DNA extracted, on a 1% agarose gel (1X TAE) run at 100V for an hour.

Lane Sample Load (µL)

1 1kb Ladder 0.5 Ladder + 2 Dye (6X) + 9.5 Milli-Q H₂O

2 CFP complete 2010 box C8 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

3 Fusion CEYFP 2007 box H5 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

4 NEYFP 2007 box J6 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

5 Fusion CEYFP 2007 box J5 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

6 CFP complete 2010 box A10 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

7 pSB-NEYFP 2010 box B6 (C1?) 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

8 Fusion CEYFP 2007 box I5 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

9 xylE 2007 box B9 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

10 CEYFP 2007 box G6 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

11 CFP complete 2010 box A6 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

12 pSB-CEYFP 2010 box C5 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

13 pSB-NEYFP 2010 box B6 (C1?) 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

14 pSB-CEYFP 2010 BOX C3 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

15 xylE 2007 box C4 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

16 CEYFP 2007 box H6 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

17 NEYFP 2007 box J6 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

Picture to come!!!!!!!!!

June 24/2010

(in lab: JV, HS, AV)

Objective:: To run a PCR of biobrick parts from out working plasmid box.

Method:

Master Mix Volume/tube (µL) Total Volume (µL)

MilliQ H₂O 12.8 448

DNA 1 -------

5X Phusion Buffer 4 140

10µM dNTP's 1 35

Forward Primer 0.5 17.5

Reverse Primer 0.5 17.5

Polymerase 0.2 7

Ran for 25 cycles on lig25 setting.
Objective:: Restriction Digest, Run on agarose gel, and ligate PCR products from June 23/10.

Method:

Six tubes for restriction digest:

Part 1 Part 2

Lane 8 (I2) Lane 4 (C1)

Lane 19 (A9) Lane 8 (I2)

Lane 19 (A9) Lane 8 (I2)

Restriction Digest Reaction Mixture:

Ingredient Volume (µL)

Plasmid DNA 2

Enzyme 0.5

Buffer 2

Milli-Q H₂O 15.5

Incubate at 37^oC for 1 hour. Then heat kill the enzymes at 80^oC for 20 minutes.

2% Agarose gel electrophoresis:

Lane Sample Load (µL)

1 50bp Ladder 1 Ladder + 2 Dye (6X) + 5 Milli-Q H₂O

2 Fus-RBS-xylE (I2); Lane 8 5 PCR sample + 2 Dye (6X) + 5 Milli-Q H₂O

3 Fus-RBS-xylE (I2) restricted; Lane 8 5 PCR sample + 2 Dye (6X) + 5 Milli-Q H₂O

4 Phu-dT (C1); Lane 4 5 PCR sample + 2 Dye (6X) + 5 Milli-Q H₂O

5 Phu-dT (C1) restricted; Lane 4 5 PCR sample + 2 Dye (6X) + 5 Milli-Q H₂O

6 Phu-pLacI (A9); Lane 19(1) 5 PCR sample + 2 Dye (6X) + 5 Milli-Q H₂O

7 Phu-pLacI (A9) restricted; Lane 19(1) 5 PCR sample + 2 Dye (6X) + 5 Milli-Q H₂O

8 Phu-pLacI (A9); Lane 19(2) 5 PCR sample + 2 Dye (6X) + 5 Milli-Q H₂O

9 Phu-pLacI (A9) restricted; Lane 19(2) 5 PCR sample + 2 Dye (6X) + 5 Milli-Q H₂O

10 Fus-RBS-xylE (I2); Lane 8(1) 5 PCR sample + 2 Dye (6X) + 5 Milli-Q H₂O

11 Fus-RBS-xylE (I2) restricted; Lane 8(1) 5 PCR sample + 2 Dye (6X) + 5 Milli-Q H₂O

12 Fus-RBS-xylE (I2); Lane 8(2) 5 PCR sample + 2 Dye (6X) + 5 Milli-Q H₂O

13 Fus-RBS-xylE (I2) restricted; Lane 8(2) 5 PCR sample + 2 Dye (6X) + 5 Milli-Q H₂O

Ran gel at 100V for 60 min and stained in EtBr for 15 min.
Picture to come!!!!!!!!!

Objective:: Run 1% agarose gel of PCR samples from June 24/10.

Lane Sample Load (µL)

1 A4-pBAD 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

2 A4-pBAD 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

3 A6-SRBS 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

4 A7-SRBS 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

5 A8-CFP Complete 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

6 A10-SRBS 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

7 B1-EYFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

8 B2-N-term tag 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

9 B4-pSB-NEYFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

10 B5-pSB-NEYFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

11 B6-CFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

12 B10-pBAD-TetR 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

13 D3 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

14 D4-C-term tag 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

15 D5-C-term tag 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

16 D6-PLacI 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

17 E2-NEYFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

18 E6-CEYFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

19 E7-CEYFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

20 1kb ladder 0.5 ladder + 2 Dye (6X) + 9.5 Milli-Q H₂O

21 E8-EYFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

22 E9-EYFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

23 E10-ECFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

24 F1-ECFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

25 F2-ECFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

26 F3-ECFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

27 F4-pBAD-TetR 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

28 F5-pBAD-TetR 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

29 G1-EYFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

30 G4-pSB-CEYFP 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

31 G6-pBAD(1) 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

32 G7-pBAD(2) 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

33 G8-N-term tag 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

33 G9-Lumazine 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

33 1kb ladder 0.5 ladder + 2 Dye (6X) + 9.5 Milli-Q H₂O

Results:

June 28/2010

(in lab: JV, HS, AV, HB)

Objective:: To restrict, run 1% agarose gel, and ligate all mms6, lumazine, xylE into pET28(a) for overexpression tests.

Method:
1) Restrict all parts and pET28(a) with NotI

2) Run on agarose gel (1%)

3) Ligate parts into pET28(a)

Parts:

from working plasmid box 2010:

A3-Lumazine
B9-Mms6
D7-xylE
D8-xylE
I10-Mms6

from pink tray:

B9-xylE
C4-xylE
G9-Lumazine

(2X) pET28(a)

Restrictions:

2µL DNA
2µL Orange Buffer
0.25µL Enzyme (NotI)
15.75µL Milli-Q H₂O

Protocol:

1) Incubate for 1 hour at 37^oC
2) Heat kill for 20 minutes at 80^oC (heat block)

Agarose Gel:

Lane Sample Load (µL)

1 1kb ladder 0.5 ladder + 2 Dye (6X) + 9.5 Milli-Q H₂O

2 Lumazine A3 RD 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

3 Lumazine A3 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

4 Mms6 I10 RD 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

5 Mms6 I10 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

6 Mms6 B9 RD 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

7 Mms6 B9 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

8 xylE D8 RD 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

9 xylE D8 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

10 xylE D7 RD 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

11 xylE D7 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

12 Lumazine G9 RD (p) 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

13 Lumazine G9 (p) 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

14 xylE B9 RD (p) 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

15 xylE B9 (p) 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

16 xylE C4 RD (p) 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

17 xylE C4 (p) 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

18 pET28(a) RD 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

19 pET28(a) RD 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

20 pET28(a) 5 DNA + 2 Dye (6X) + 5 Milli-Q H₂O

Ran gel at 100V for 90 minutes

Results:pET28(a) bands are all smeared, and are not useful from inserting parts.

June 30/2010

(in lab: JV)

Objective:: Isolate plasmid DNA from DH5α

Method:Used Kothe Maxiprep protocol.
Cell Pellet Weights:

xylE = 1.15g
Mms6 = 1.13g
pET28(a) = 0.67g
lumazine synthase = 1.1g

Results:

Retrieved from "http://2010.igem.org/Team:Lethbridge/Notebook/Lab_Work/June"

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

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 EYFP (B1)	10µL DNA 2µL Dye	Restricted Fusion CEYFP (E3)	10µL DNA 2µL Dye
3	Unrestricted EYFP (B1)	10µL DNA 2µL Dye	Unrestricted Fusion CEYFP (E3)	10µL DNA 2µL Dye
4	Restricted pSB-CEYFP (B5)	10µL DNA 2µL Dye	Restricted Fusion CEYFP (E4)	10µL DNA 2µL Dye
5	Unrestricted pSB-CEYFP (B5)	10µL DNA 2µL Dye	Unrestricted Fusion CEYFP (E4)	10µL DNA 2µL Dye
6	Restricted ECFP (F2)	10µL DNA 2µL Dye	Restricted EYFP (E10)	10µL DNA 2µL Dye
7	Unrestricted ECFP (F2)	10µL DNA 2µL Dye	Unrestricted EYFP (E10)	10µL DNA 2µL Dye
8	Restricted pSB-CEYFP (G4)	10µL DNA 2µL Dye	Restricted pSB NEYFP (B4)	10µL DNA 2µL Dye
9	Unrestricted pSB-CEYFP (G4)	10µL DNA 2µL Dye	Unrestricted pSB NEYFP (B4)	10µL DNA 2µL Dye
10	Restricted EYFP (G1)	10µL DNA 2µL Dye	Restricted ECFP (F3)	10µL DNA 2µL Dye
11	Unrestricted EYFP (G1)	10µL DNA 2µL Dye	Unrestricted ECFP (F3)	10µL DNA 2µL Dye
12	Restricted NEYFP (E2)	10µL DNA 2µL Dye	pBad-TetR (F5)	10µL DNA 2µL Dye
13	Unrestricted NEYFP (E2)	10µL DNA 2µL Dye	Restricted Fusion CEYFP (E5)	10µL DNA 2µL Dye
14	Restricted pBad-TetR (B10)	10µL DNA 2µL Dye	Unrestricted Fusion CEYFP (E5)	10µL DNA 2µL Dye
15	Unrestricted pBad-TetR (B10)	10µL DNA 2µL Dye	pBad-TetR (F4)	10µL DNA 2µL Dye
16	Restricted CEYFP (E6)	10µL DNA 2µL Dye	Restricted pSB1T3	10µL DNA 2µL Dye
17	Unrestricted CEYFP (E6)	10µL DNA 2µL Dye	Unrestricted pSB1T3	10µL DNA 2µL Dye
18	Restricted NEYFP (E1)	10µL DNA 2µL Dye		10µL DNA 2µL Dye
19	Unrestricted NEYFP (E1)	10µL DNA 2µL Dye
20	Restricted ECFP (F1)	10µL DNA 2µL Dye
21	Unrestricted ECFP (F1)	10µL DNA 2µL Dye
22	Restricted EYFP (E9)	10µL DNA 2µL Dye
23	Unrestricted EYFP (E9)	10µL DNA 2µL Dye
24	Restricted CEYFP (E7)	10µL DNA 2µL Dye
25	Unrestricted CEYFP (E7)	10µL DNA 2µL Dye
26	Restricted EYFP (E8)	10µL DNA 2µL Dye
27	Unrestricted EYFP (E8)	10µL DNA 2µL Dye

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+</a>
+</th>
+<th><a href="https://2010.igem.org/Team:Lethbridge/Notebook/Lab_Work/June">
+<img src="https://static.igem.org/mediawiki/2010/8/80/UofLjunebutton.jpg" width="80"/>
+</a>
+</th>
+<th><a href="https://2010.igem.org/Team:Lethbridge/Notebook/Lab_Work/July">
+<img src="https://static.igem.org/mediawiki/2010/5/53/UofLjulybutton.jpg" width="60"/>
+</a>
+</th>
+<th><a href="https://2010.igem.org/Team:Lethbridge/Notebook/Lab_Work/August">
+<img src="https://static.igem.org/mediawiki/2010/1/15/UofLaugustbutton.jpg" width="60"/>
+</a>
+</th>
+<th><a href="https://2010.igem.org/Team:Lethbridge/Notebook/Lab_Work/September">
+<img src="https://static.igem.org/mediawiki/2010/4/4d/UofLseptemberbutton.jpg" width="60"/>
+</a>
+</th>
+<th><a href="https://2010.igem.org/Team:Lethbridge/Notebook/Lab_Work/October">
+<img src="https://static.igem.org/mediawiki/2010/4/4e/UofLoctoberbutton.jpg" width="60"/>
+</a>
+</th>
+<tr>
+</table>
+</center>
+</body>
+</html>
+<hr>
-|}
+<BLOCKQUOTE>
-Back to [[Team:Lethbridge/Notebook|Notebook]]<br>
-Back to [[Team:Lethbridge/Notebook/Lab_Work|Lab Work]]
-=June 2010=
+=<font color="white">June 2010=
-==June 1/2010==
+==<font color="white">June 1/2010==
 JV quantified the amount of DNA in gels run to date using ImageJ software. Results to be posted in [[Team:Lethbridge/Notebook/Working_Plasmids|working plasmids box]].<br>
@@ Line 68: / Line 218: @@
 *BglII Endonuclease (Bba_K112106)<br>
-==June 2/2010==
+==<font color="white">June 2/2010==
 (In Lab: JV)<br>
@@ Line 141: / Line 291: @@
 Killed enzymes by incubating reactions for 10 minutes at 80<sup>o</sup>C</ul>
-==June 2/2010 - Evening==
+==<font color="white">June 2/2010 - Evening==
 <b>Objective:</b> Set up new ligations of pLacI and sRBS-Lum-dT according to Tom Knight's protocol. Previous ligation had very little DNA.<br>
 <b>Relevant Information:</b><br>
@@ Line 190: / Line 340: @@
 Incubate for 20 minutes at 80<sup>o</sup>C to heat kill<br>
-==June 3/2010==
+==<font color="white">June 3/2010==
 Carried out protocol described in June 2/2010 - Evening<br>
 Analyzed results on 1% agarose gel.Load order as follows:<br>
@@ Line 220: / Line 370: @@
-==June 3/2010 - Evening==
+==<font color="white">June 3/2010 - Evening==
 <b>Objective:</b> Repeat restriction of pSB1T3 and ligate with pLacI and sRBS-Lum-dT. Previous ligations all used up on gel.<br>
 <b>Method:</b><br>
@@ Line 265: / Line 415: @@
 <b>Continue Ligation on Saturday (See below).</b><br>
-==June 5/2010 ==
+==<font color="white">June 5/2010 ==
 (In the lab:AS)<br>
 <b>Objective:</b> Ligate restriction products from June 3/2010.<br>
@@ Line 289: / Line 439: @@
-==June 6/2010 ==
+==<font color="white">June 6/2010 ==
 (In Lab: JV, HS)<br>
@@ Line 321: / Line 471: @@
 None of the plates showed any growth.
-==June 7/2010 ==
+==<font color="white">June 7/2010 ==
 (In Lab: JV, HB, TF, AV)<br>
@@ Line 386: / Line 536: @@
 <tr><td>10</td><td>Empty</td><td></td></tr></table>
-Ran at 100V for 72 min.
+Ran at 100V for 72 min.<br>
-==June 8/2010==
+<font color ="Red">IMAGE TO COME!!!!!!</font><br>
+==<font color="white">June 7/2010 - Evening ==
+(In Lab: AS, KG)<br>
+<b>Objective:</b><br> Ligation of:<br>
+*pBAD-TetR (F5) + CEYFP (E6)
+*pBAD-TetR (F5) + NEYFP (E1)
+*pBAD-TetR (F5) + pSB-NEYFP (B4)
+*pBAD-TetR (F5) + Fusion-CEYFP (E7)
+*pBAD-TetR (F5) + Fusion-CEYFP (E3)
+*pBAD-TetR (F5) + CEYFP (E7)
+*pBAD-TetR (F5) + NEYFP (E2)
+*pBAD-TetR (F5) + pSB-CEYFP (B5)
+*pBAD-TetR (F5) + Fusion-CEYFP (E5)
+*pBAD-TetR (F5) + pSB-CEYFP (G4)
+*pBAD-TetR (F4) + CEYFP (E7)
+*pBAD-TetR (F4) + NEYFP (E1)
+*pBAD-TetR (F4) + pSB-NEYFP (B4)
+*pBAD-TetR (F4) + pSB-CEYFP (B5)
+*pBAD-TetR (F4) + CEYFP (E6)
+*pBAD-TetR (F4) + Fusion-CEYFP (E4)
+*pBAD-TetR (F4) + Fusion-CEYFP (E3)
+*pBAD-TetR (F4) + pSB-CEYFP (G4)
+*pBAD-TetR (F4) + Fusion-CEYFP (E5)
+*pBAD-TetR (F4) + NEYFP (E2)
+*pBAD-TetR (B10) + pSB-NEYFP (B4)
+*pBAD-TetR (B10) + pSB-CEYFP (G4)
+*pBAD-TetR (B10) + NEYFP (E1)
+*pBAD-TetR (B10) + CEYFP (E6)
+*pBAD-TetR (B10) + CEYFP (E7)
+*pBAD-TetR (B10) + Fusion-CEYFP (E4)
+*pBAD-TetR (B10) + pSB-CEYFP (B5)
+*pBAD-TetR (B10) + Fusion-CEYFP (E5)
+*pBAD-TetR (B10) + Fusion-CEYFP (E3)
+*pBAD-TetR (B10) + NEYFP (E2)
+<b>Method:</b><br>
+<font color ="Red">FILL ME IN!!!!!!</font><br>
+==<font color="white">June 8/2010==
 (In the lab: JV, AV)<br>
 <b>Objective:</b> Follow the overexpression of our pLacI-sRBS-Lum-dT construct.<br>
@@ Line 502: / Line 692: @@
 Looks like the mms6 DNA was not cut at all. Therefore is doubtful that the ligations will work.<br><br>
-==June 8/2010 - Evening==
+==<font color="white">June 8/2010 - Evening==
 <b>Objective:</b> Transform pLacI-sRBS-Lum-dT constructs assembled via three antibiotic assembly on June 3/2010. Also transform mms6-dT constructs assembled today using old insertion method.<br>
 <b>Method:</b> Follow [[Team:Lethbridge/Notebook/Protocols|transformation protocol]].
 <b>Results:</b> No colonies anywhere<br>
-==June 9/2010==
+==<font color="white">June 9/2010==
 (in the lab: TF, JV)<br>
 <b>Objective:</b> Transform mms6-dT ligation reactions from June 8/2010.<br>
@@ Line 517: / Line 707: @@
 <b>Results:</b> No transformants on plates.<br><br>
-==June 10/2010==
+==<font color="white">June 10/2010==
 (In the lab: AV, HB, JV)<br>
 <b>Objective:</b> Repeat ligation of mms6 (B9,D9,D10) and dT (C1).<br>
@@ Line 572: / Line 762: @@
 *B0010-B0012: 120 colonies
-==June 14/2010 Evening==
+==<font color="white">June 14/2010 Evening==
 (In the lab: TF, DM, HS)<br>
 <b>Objective:</b> Restriction Digest of RBS-xylE with EcoRI and SpeI<br>
@@ Line 596: / Line 786: @@
 *Incubate overnight
-==June 15/2010==
+==<font color="white">June 15/2010==
 (In the lab: JV)<br>
@@ Line 656: / Line 846: @@
 DNA was then purified using the protocol for purification of PCR products (BioBasic). DNA was eluted with 35&micro;L of elution buffer.<br>
-==June 15/2010 Evening==
+==<font color="white">June 15/2010 Evening==
 (In the lab: AS)<br>
@@ Line 697: / Line 887: @@
 <b>Results: </b>Everything cuts exactly as it should. Continue with ligation and analysis. <font color ="Red">IMAGE TO COME!!!!</font><br>
-==June 16/2010==
+==<font color="white">June 16/2010==
 (in lab: JV)
 <b>Objective: </b>To miniprep Adam's overnight cultures of xylE and rbs. Completing this will give us a working stock of this plasmid.<br>
@@ Line 714: / Line 904: @@
 <b>Results:</b> There wasn't any growth after overnight incubation. Possibility of an antibiotic mix-up.
-==June 16/2010 Evening==
+==<font color="white">June 16/2010 Evening==
 (in lab: ADS)
@@ Line 781: / Line 971: @@
 &micro;L of each VF2 & VR primers (10&micro;L) -> send 65&micro;L
-==June 17/2010==
+==<font color="white">June 17/2010==
 (in lab: JV, HB)
 <b>Objective:</b>Run Agarose gel of overnight samples from June 16/10 to test T4 DNA ligase<br>
@@ Line 803: / Line 993: @@
 <font color ="Red">IMAGE TO COME!!!!</font><br>
-==June 17/2010 Evening==
+==<font color="white">June 17/2010 Evening==
 (in lab: JS, AS, KG)<br>
@@ Line 828: / Line 1,018: @@
 *controls (no forward or reverse primer and no DNA)<br>
-==June 18/2010==
+==<font color="white">June 18/2010==
 (in lab: JV)<br>
@@ Line 849: / Line 1,039: @@
 <br>
-==June 21/2010==
+==<font color="white">June 21/2010==
 (in lab: JV)<br>
@@ Line 875: / Line 1,065: @@
 <b>Results:</b>PCR samples were run on a gel (1% 1XTAE) with the PCR samples from June 22/10. This gel was run on June 22/10<br>
-==June 22/2010==
+==<font color="white">June 22/2010==
 (in lab: JV, HS)<br>
@@ Line 943: / Line 1,133: @@
 Ran the gel for 40 minutes at 100V.<br>
-==June 22/2010 Evening==
+==<font color="white">June 22/2010 Evening==
 (in lab: KG, AS)<br>
@@ Line 1,000: / Line 1,190: @@
 <tr><td>Imitrages polymerase</td><td>0.2</td></tr></table><br>
-==June 23/2010==
+==<font color="white">June 23/2010==
 (in lab: JV, HS)<br>
@@ Line 1,058: / Line 1,248: @@
 *all Phusion tubes are <font color ="Blue">blue</font><br>
-<b>Results:</b>: <font color ="Red">Picture to come!!!!!!!!!</font><br>
+<b>Results:</b>
+<font color="red">IMAGE!!!</font>
@@ Line 1,095: / Line 1,286: @@
 <font color ="Red">Picture to come!!!!!!!!!</font><br>
-==June 24/2010==
+==<font color="white">June 24/2010==
 (in lab: JV, HS, AV)<br>
@@ Line 1,197: / Line 1,388: @@
 <tr><td>33</td><td>1kb ladder</td><td>0.5 ladder + 2 Dye (6X) + 9.5 Milli-Q H<sub>2</sub>O</td></tr>
 </table><br>
+<b>Results:</b> [[image:Lethbridge_100624PCR.JPG|200px]]
-<font color ="Red">Picture to come!!!!!!!!!</font><br>
+==<font color="white">June 28/2010==
-==June 28/2010==
 (in lab: JV, HS, AV, HB)<br>
-<b>Objective:</b>: To restrict, run 1% agarose gel, and ligate all mms6, lumazine, xylE into PET28(a) for overexpression tests.<br>
+<b>Objective:</b>: To restrict, run 1% agarose gel, and ligate all mms6, lumazine, xylE into pET28(a) for overexpression tests.<br>
 <b>Method:</b><br>
+) Restrict all parts and pET28(a) with NotI<br>
+) Run on agarose gel (1%)<br>
+) Ligate parts into pET28(a)<br>
+Parts: <br>
+:from working plasmid box 2010:<br>
+*A3-Lumazine
+*B9-Mms6
+*D7-xylE
+*D8-xylE
+*I10-Mms6
+:from pink tray:<br>
+*B9-xylE
+*C4-xylE
+*G9-Lumazine
+:(2X) pET28(a)<br>
+Restrictions:<br>
+*2&micro;L DNA
+*2&micro;L Orange Buffer
+*0.25&micro;L Enzyme (NotI)
+*15.75&micro;L Milli-Q H<sub>2</sub>O
+Protocol:<br>
+*1) Incubate for 1 hour at 37<sup>o</sup>C
+*2) Heat kill for 20 minutes at 80<sup>o</sup>C (heat block)<br>
+Agarose Gel:<br>
+<table><table border ="3">
+<tr><td><b>Lane</b></td><td><b>Sample</b></td><td><b>Load (&micro;L)</b></td></tr>
+<tr><td>1</td><td>1kb ladder</td><td>0.5 ladder + 2 Dye (6X) + 9.5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>2</td><td>Lumazine A3 RD</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>3</td><td>Lumazine A3</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>4</td><td>Mms6 I10 RD</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>5</td><td>Mms6 I10</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>6</td><td>Mms6 B9 RD</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>7</td><td>Mms6 B9</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>8</td><td>xylE D8 RD</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>9</td><td>xylE D8</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>10</td><td>xylE D7 RD</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>11</td><td>xylE D7</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>12</td><td>Lumazine G9 RD (p)</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>13</td><td>Lumazine G9 (p)</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>14</td><td>xylE B9 RD (p)</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>15</td><td>xylE B9 (p)</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>16</td><td>xylE C4 RD (p)</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>17</td><td>xylE C4 (p)</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>18</td><td>pET28(a) RD</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>19</td><td>pET28(a) RD</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr>
+<tr><td>20</td><td>pET28(a)</td><td>5 DNA + 2 Dye (6X) + 5 Milli-Q H<sub>2</sub>O</td></tr></table>
+Ran gel at 100V for 90 minutes<br>
+<b>Results:</b>pET28(a) bands are all smeared, and are not useful from inserting parts.<br>
+[[image:Lethbridge_100628AV (2).JPG|200px]]<br>
+==<font color="white">June 30/2010==
+(in lab: JV)<br>
+<b>Objective:</b>: Isolate plasmid DNA from DH5&alpha;<br>
+<b>Method:</b>Used Kothe Maxiprep protocol.<br>
+Cell Pellet Weights:<br>
+*xylE = 1.15g
+*Mms6 = 1.13g
+*pET28(a) = 0.67g
+*lumazine synthase = 1.1g<br>
+<b>Results:</b><br>

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

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

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

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

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

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

Component	Volume (µL)
Restriction Enzyme (XbaI)	0.25
Buffer (Tango)	2
Plasmid DNA	2
MilliQ H₂O	15.75

Lane	Sample	Load (µL)
1	1kb ladder	2 ladder + 2 dye (6X) + 8 MilliQ H₂O
2	J5-pLacI-SRBS-Lumazine-dT(1)	10 DNA + 2 Dye (6X)
3	J5-pLacI-SRBS-Lumazine-dT(1)restricted	10 DNA + 2 Dye (6X)
4	J6-pLacI-SRBS-Lumazine-dT(2)	10 DNA + 2 Dye (6X)
5	J5-pLacI-SRBS-Lumazine-dT(2)restricted	10 DNA + 2 Dye (6X)
6	pSB1T3	10 DNA + 2 Dye (6X)
7	pSB1T3 restricted	10 DNA + 2 Dye (6X)
8	Empty
9	Empty
10	Empty

Time	OD₆₀₀ F1	OD₆₀₀ E10
0	0.118	0.103
30	0.133	0.111
30	0.145	0.116
90
120	0.160	0.124
150	0.120	0.093
180	0.129	0.100
210	0.145	0.122
240	0.158	0.145
270	0.171	0.178
300	0.194	0.222
330	0.223	0.280
360	0.252	0.364
390	0.296	0.458
420	0.338	0.557^†
450	0.394	0.656
480	0.453	0.675
510	0.530	0.688
540	0.598^†	0.706
600	0.633	0.752
660	0.653
720	0.679
∞	1.278

Name	Concentration (ng/µL)	Dilution Factor	Final Concentration (ng/µL)
A8-CFP complete	1395	1/5	280
B4-pSB NEYFP	1105	1/5	240
B5-pSB CEYFP	1055	1/5	210
B6-CFP complete	1285	1/5	260
D7-xylE	1820	1/10	182
D8-xylE	420	1/2	210
E1-NEYFP	235	1/2	117.5
E2-NEYFP	2980	1/10	300
E3-Fusion CEYFP	255	1/2	122.5
E4-Fusion CEYFP	490	1/2	245
E5-Fusion CEYFP	335	1/2	335
E6-CEYFP	1605	1/10	160
E7-CEYFP	1930	1/10	190
G4-pSB CEYFP	340	1/4	85
G5-CFP complete	355	1.4	89

Time	OD F1 (600λ)	OD E10 (600λ)
0	0.078	0.072
60	0.122	0.110
90	0.128	0.125
120	0.140	0.138
150	0.149	0.157
180	0.169	0.183
210	0.205	0.230
240	0.243	0.276
270	0.278	0.323
300	0.317	0.398
330	0.394	0.428
360	0.394	0.480
390	0.441	0.553
400	----	0.594 (induced)
410	0.502	-----
450	0.580 (induced)	0.736
510	0.804	1.005
570	1.065	1.066
630	1.053	1.043
∞	0.055 (1/10 dilution)	0.078 (1/10 dilution)

Master Mix 1	Volume/tube (µL)	Total Volume (µL)
MilliQ H₂O	10.8	226.8
DNA	2	4
5X Phusion HF Buffer	4	84
10µM dNTP's	1	21
Forward Primer (VF2)	1	21
Reverse Primer (VR)	1	21
Fimnzzymes polymerase	0.2	4.2

Master Mix 2	Volume/tube (µL)	Total Volume (µL)
MilliQ H₂O	10.8	226.8
DNA	2	4
5X Econo Taq Buffer	4	84
10µM dNTP's	1	21
Forward Primer (VF2)	1	21
Reverse Primer (VR)	1	21
Imitrages polymerase (Econo Taq)	0.2	4.2

Master Mix for pSB1A3	Volume/tube (µL)	Total Volume (µL)
MilliQ H₂O	10.8	31
DNA	1	20
5X Phusion Buffer	4	10
10µM dNTP's	1	2.5
Primer (SB-prep-2Ea)	1	2.5
Primer (SB-prep-3P)	1	2.5
Fimnzzymes polymerase	0.2	0.5

Part 1	Part 2
Lane 8 (I2)	Lane 4 (C1)
Lane 19 (A9)	Lane 8 (I2)
Lane 19 (A9)	Lane 8 (I2)