Difference between revisions of "Team:Edinburgh/Notebook/HeroinPurity"

Latest revision as of 18:59, 20 November 2015

Heroin Purity

Week 1
01/06
Order MorA (morphine dehydrogenase). Sequence from Professor Chris French.

Week 4
23/06
Digest the MorA (from IDT) as well as the LacI expression vector (BBa_K314103) and pSB1C3 (BBa_J04450). For MorA into LacI use XbaI/PstI, for LacI use SpeI/PstI, MorA into pSB1C3 use EcoRI HF/PstI, and pSB1C3 use EcoRI HF/PstI.

PCR purification for MorA. Gel purification for pSB1C3 and LacI. Nanodrop.

24/06
Ligate LacI to MorA (XbaI) and pSB1C3 and MorA (EcoRI/PstI), control ligations of backbones only.

Transform 3µL ligation reaction into E.coli Dh5α cells.

25/06
No growth on the control plates. Definite colonies on ligation experiments. Inoculate colonies.

26/06
No growth in culture. Streak 8 colonies from each plate onto new plates to grow at room temperature (18ºC) over the weekend.

Week 5
29/06
No growth on streaked plates.
Digest MorA for LacI (XbaI/PstI) and pSB1C3 (EcoRI HF/PstI) as well as re-digesting LacI (SpeI/PstI) and pSB1C3 (EcoRI HF/PstI).
PCR purify LacI and MorA (both digestions).
Gel purify pSB1C3.
Nanodrop.

Ligate MorA into LacI and pSB1C3 again for an overnight reaction at 16ºC.

30/06
Transform ligation results.

01/07
Transformations all worked except for MorA in pSB1C3.

Try different restriction sites to see if that makes a difference. Digest MorA with EcoRI HF/SpeI and XbaI/PstI. Digest pSB1C3 with EcoRI HF/SpeI and XbaI/PstI.
Gel purify the pSB1C3 backbones. PCR purify the MorA inserts. Nanodrop.

Ligate pSB1C3 (EcoRI HF/SpeI) to MorA (EcoRI HF/SpeI) and pSB1C3 (XbaI/PstI) to MorA (XbaI/PstI).

02/07
Sequence LacI+MorA1 and LacI+MorA2. Diagnostic digest LacI+MorA1 and LacI+MorA2.

03/07
Try putting MorA into pSB1C3 using the linearized backbone from the distribution kit. Digest, ligate, transform.

04/07
Growth appeared on all of the ligated plates with no growth on the controls.

05/07
Inoculate colonies from the plate.

Week 6
06/07
Miniprep cultures. Nanodrop.

Diagnostic digest.

07/07
Sent pSB1C3+MorA1, pSB1C3+MorA2, LacI+MorA1 and LacI+MorA2 off for sequencing.

08/07
Digest CBDs (BBa_K1321339, BBa_K1321340, BBa_K1321003 and BBa_K1321002) with AgeI/SpeI for N terminal fusions and XbaI/NgoMIV for C terminal fusions. Digest MorA with XbaI/AgeI for C terminal fusions and NgoMIV/SpeI for N terminal fusions.
Treat CBDs with Antarctic Phosphatase.
PCR purify CBDs. (Note: could not gel purify MorA because it was not fully cut, so not much of a band to purify).

Transform LacI+MorA into BL21 for expression.
Digest pSB1C3+MorA overnight for a C (XbaI/AgeI) and N (NgoMIV/SpeI) terminal fusion.

09/07
LacI+MorA seems like it went into BL21.

Gel purify the overnight digest. Nanodrop.

Make a batch culture of LacI+MorA in BL21.

10/07
Ligate all of the CBDs to MorA with both N and C terminal fusions.
Transform the ligations.
11/07
Some ligations appeared to have potentially worked. Place the plates in 4ºC. Miniprep and make glycerols of cultures. Nanodrop.

12/07
Make a batch culture of LacI+MorA in BL21.

Inoculate transformants that appeared to have worked.

Week 7
13/07
Make glycerols of cultures, miniprep and nanodrop.

Diagnostic digest.

Digest MorA again for both N (NgoMIV/SpeI) and C (XbaI/AgeI) terminal fusions. Digest the four CBDs (BBa_K1321339, BBa_K1321340, BBa_K1321003 and BBa_K1321002) for N (AgeI/SpeI) and C (XbaI/NgoMIV) terminal fusions.

Ligate MorA to CBDs.

14/07
Transform ligations.

Make two batch cultures of LacI+MorA in BL21. Each has 500 µL. Induce with IPTG.

15/07
It appears that all of the transformations worked. Inoculate transformations.

16/07
Inoculations all grew except BBa_K1321339+MorAC (1). Miniprep and make glycerols of inoculations that grew. Nanodrop.

Diagnostic digest.

Week 8
20/07
Sequence BBa_K1321340+MorA C2, BBa_K1321340+MorA N3, BBa_K1321003+MorA C1, BBa_K1321002+MorA C2, BBa_K1321002+MorA N2, BBa_K1321003+MorA N3 and BBa_K1321339+MorA N4.

Transform heroin esterase gene into Top10s.

21/07
Inoculate heroin esterase.

22/07
Nanodrop heroin esterase 1 and 2.

Try to put heroin esterase into pSB1C3 and into LacI using EcoRI/PstI and XbaI/PstI respectively.

Treat backbones with Antarctic Phosphatase. Ligate.

23/07
Digest heroin esterase (XbaI/PstI) and LacI (SpeI/PstI). Ligate. Transform.

Inoculate transformants.

24/07
Nanodrop LacI + heroin esterase 1, 2 and pSB1C3 + heroin esterase 1 and 2.

Diagnostic digest. Diagnostic digest was inconclusive due to bands bleaching out.

26/07
Inoculate everything that did not show up on the diagnostic digest.

Week 9
27/07
Make glycerols of all of the cultures, miniprep cultures and nanodrop.

Diagnostic digest.

28/07
Fuse heroin esterase to BBa_K1321339, BBa_K1321340, BBa_K1321003 and BBa_K1321002 on both the N and C terminals. The heroin esterase is digested with XbaI/AgeI for C terminal and NgoMIV/SpeI for N terminal. The CBDs are digested with XbaI/NgoMIV for C terminal and AgeI/SpeI for N terminal fusions.
Send of pSB1C3 + heroin esterase 3 for sequencing.
Try to put MorA fusions (CBDs+MorA N and C terminal) in pSB1A3 + LacI using XbaI/PstI for the fusions and SpeI/PstI for the LacI backbone. Treat backbone with Antarctic Phosphatase and then ligate.

29/07
Digest CBD fusions and pSB1C3 + heroin esterase for fusions into LacI.
Inoculate transformants from 28/07.

30/07
Miniprep cultures and nanodrop.

Diagnostic digest. No insert visible on gel.
Inoculate LacI+BBa_K1321340+MorA C1 and LacI+BBa_K1321340+MorA C2.

31/07
Fuse heroin esterase to BBa_K1321339, BBa_K1321340, BBa_K1321003 and BBa_K1321002 on the C terminal. The heroin esterase for C terminal is digested with EcoR1/Age1. The CBDs are digested with EcoR1/NgoMIV.
Digest CBDs + MorA and pSB1C3 + heroin esterase for fusion into LacI. CBD + MorA fusions and pSB1C3 heroin esterase were digested with Xba1/Pst1. LacI was digested with Spe1/Pst1.
Antarctic phosphatase treat the CBDs and LacI.
Ligate with appropriate controls and transform.
Make glycerol stocks, miniprep and nanodrop cultures.

Diagnostic digest. Indicates the presence of insert.

02/08
Inoculate successful transformants from 31/08

Week 10
03/08
Make glycerols, miniprep and nanodrop cultures.

Diagnostic digest.
Send LacI+BBa_K1321340+MorA C1 and LacI+BBa_K1321340+MorA C2 for sequencing.
Transform LacI + MorA into E.coli strain BL21.

04/08
Sequence BBa_K1321340+heroin esterase C1, BBa_K1321340+heroin esterase C2, BBa_K1321003+heroin esterase C2 and BBa_K1321002+heroin esterase C2.
Inoculate LacI + MorA in BL21.

05/08
Digest heroin esterase gBlock with Xba1/Age1 for fusion to the C terminal of BBa_K1321339. CBD was digested with Xba1/Spe1.
Antarctic phosphatase CBD, ligate and transform.

06/08
Inoculate successful transformants.
07/08
Fuse LacI promoter into MorA + CBD fusions. Digest LacI insert with EcoR1/Spe1. Digest CBD + MorA fusions with EcoR1/Xba1.
No phosphatase treatment.
Ligate and transform.
Make glycerols, miniprep and nanodrop.

09/08
Inoculate successful transformants.

Week 11
10/08
Make glycerols, then miniprep and nanodrop cultures.

Diagnostic digest.

11/08
Sequence BBa_K1321339+heroin esterase, LacI+BBa_K1321003+MorA C2, LacI + BBa_K1321002+MorA C2, LacI+BBa_K1321340+MorA N1 and LacI+BBa_K1321003+MorA N1.

13/08
Fuse heroin esterase and MorA to CBDCipA at both N and C terminals. Digest heroin esterase and MorA with NgoMIV/Pst1 for N terminal fusion and with EcoR1/Age1 for C terminal fusion. Digest CBD CipA with Age1/Pst1 for N terminal fusions and EcoR1/NgoMIV for C terminal fusions.
Fuse LacI promoter into heroin esterase. Digest heroin esterase with EcoR1/Xba1, and digest the LacI insert with EcoR1/Spe1. Phosphatase treat the digestions
Ligate and transform.

14/08
Retry fusing LacI to heroin esterase using the same enzymes. Phosphatase treat, ligate and transform.

16/08
Inoculate successful transformants from 13/08 and 14/08.

Week 12
17/08
Fuse LacI into CBD MorA fusions, namely BBa_K1321340+MorA C2, BBa_K1321002 MorA N2, BBa_K1321339+MorA N4 and BBa_K1321339+MorA C2. Digest LacI with EcoR1/Spe1 and digest the CBD MorA fusions with EcoR1/Xba1.
Antarctic phosphatase, ligate and transform into Top10s.
Make glycerols and miniprep cultures from 16/08. Nanodrop.

Diagnostic digest.

18/08
Sequence LacI + heroin esterase, CBDCipA + heroin esterase C and CBDCipA + MorA C.
Retry failed heroin esterase to CBD fusions, namely BBa_K1321339+heroin esterase N, BBa_K1321340+heroin esterase N, BBa_K1321003+heroin esterase N, BBa_K1321002 + heroin esterase N and BBa_K1321339+heroin esterase C. Digest CBDs with Age1/Pst1 for N terminal fusions and EcoR1/NgoMIV for C terminal fusions. Digest heroin esterase with NgoMIV/Pst1 for N terminal fusions and with EcoR1/Age1 for C terminal fusions. Phosphatase treat, ligate and transform into Top10s.
Amplify heroin esterase by PCR, PCR purify and nanodrop.

Diagnostic digest showed PCR amplified the correct sequence.
Inoculate successful transformants from 17/08

19/08
Make glycerols, miniprep and nanodrop cultures.

Diagnostic Digest indicated the presence of insert in all but BBa_K863111 fusions.
Amplify MorA by PCR, PCR purify and nanodrop.

Diagnostic digest showed PCR amplified the correct sequence.
Inoculate successful transformants.

20/08
Sequence LacI+BBa_K1321339+MorA N 1, LacI+BBa_K1321339+ MorA N 2, LacI + BBa_K1321339+ MorA C 1, LacI+BBa_K1321339+MorA C 2, LacI+BBa_K1321340+MorA C 1 and LacI+BBa_K1321340+MorA C 2.
Fuse LacI promoter into MorA and heroin esterase CBD fusions. Digest LacI with EcoR1/Spe1. Digest MorA and heroin esterase with EcoR1/Xba1. Phosphatase treat, ligate and transform into Top10s.
Make glycerols, miniprep and nanodrop cultures.

Diagnostic digest indicated no insert was present.

21/08
Retry fusion of heroin esterase and MorA to CBDs. Digest CBDs with Age1/Pst1 for N terminal fusions and with EcoR1/NgoMIV for C terminal fusions. Digest inserts with NgoMIV/Pst1 for N terminal fusions and with EcoR1/Age1 for C terminal fusions. Phosphatase treat, ligate and transform into Top10s.
Transform LacI+BBa_K1321340+MorA N1, LacI+BBa_K1321003+ MorA N1, LacI + BBa_K1321003+MorA C2, LacI+BBa_K1321002+MorA C2 and LacI+heroin esterase into BL21s.

23/08
Inoculate successful transformants from 20/08 and 21/08.
Make starter cultures for BL21 transformants.

Week 13
24/08
Retry failed fusions for heroin esterase to CBDs, and MorA to CBDCipA. Digest CBDs with Age1/Pst1 for N terminal fusions and with EcoR1/NgoMIV for C terminal fusions. Digest inserts with NgoMIV/Pst1 for N terminal fusions and with EcoR1/Age1 for C terminal fusions. Treat with antarctic phosphatase for 1 hour. Ligate and transform into Top10s.
Transform LacI+BBa_K1321339+MorA N1, LacI+BBa_K1321339+MorA C2 and LacI+ BBa_K1321340+MorA C1 into BL21s.
Make glycerols and miniprep transformants from 20/08. Nanodrop.

Diagnostic digest. Digest indicated the presence of inserts in some of the samples.

25/08
Sequence LacI+BBa_K1321340+heroin esterase C1, LacI+BBa_K1321003+heroin esterase C1 and LacI+BBa_K1321002+heroin esterase C1.
Fuse LacI into CBDCipA+MorA C2 and BBa_K1321002+MorA N2. Digest LacI with EcoR1/Spe1, and digest the backbone with EcoR1/Xba1. Phosphatase treat and ligate. Transform into Top10s.
Inoculate successful transformants.

26/08
Retry fusions to heroin esterase.
Digest the heroin esterase with heroin esterase with NgoMIV/Pst1 for N terminal fusions and with EcoR1/Age1 for C terminal fusions. Digest CBD with Age1/Pst1 for N terminal fusions and with EcoR1/NgoMIV for C terminal fusions.
Phosphatase treat CBDs for 1 hour then ligate and transform into Top10s.

Make glycerols of cultures, then miniprep and nanodrop.

Diagnostic digest indicated presence of insert in 1 fusion.

Inoculate successful transformants.

27/08
Sequence BBa_K1321339+heroin esterase C 1 and 2.
Make glycerols from the cultures. Miniprep and nanodrop.
Diagnostic digest indicated presence of insert in one fusion.

28/08
Sequence CBDCipA + MorA C2 + LacI (1).
Make glycerols of cultures, miniprep and nanodrop.

Diagnostic digest indicated the presence of insert in certain fusions.

Week 13
31/08
Transform MorA into BL21s.
Transform pT7 MorA and pMorA 1 from Professor Chris French into BL21s.

01/09
Sequence CBDCipA+MorA C2+LacI(1), CBDCipA MaoA C(1), CBDCipA+heroin esterase N(1), CBDCipA+heroin esterase N(2), CBDCipA+heroin esterase C(1), CBDCipA+heroin esterase C(2), BBa_K1321339+heroin esterase N(1), BBa_K1321339+heroin esterase N(2), BBa_K1321003+heroin esterase N(2), BBa_K1321002+heroin esterase N(1), BBa_K1321002+heroin esterase N(2).

Week 14
07/09
Insert LacI into CBD fusions. Digest LacI with EcoRI/Spe1, and digest CBD fusions with EcoR1/Xba1. Phosphatase treat all CBD fusions, then ligate and transform.

08/09
Inoculate successful transformants.
Transform LacI+CBDCipA+MorA C(1) into E.coli BL21 cells.

09/09
Make glycerols of cultures, then miniprep and nanodrop.

Diagnostic digest showed insert was present in some fusions.

Ran the Heroin esterase assay

10/09
Ran the Morphine dehydrogenase (MDH) assay

11/09

Ran the Morphine dehydrogenase (MDH) assay again

Created colour detection gradient

12/09

Ran the Morphine dehydrogenase (MDH) assay again

Re-created colour detection gradient

Week 15
14/09
Sequence LacI+BBa_K1321002+heroin esterase N1 and LacI+BBa_K1321339+heroin esterase C1.

15/09

Ran all sequence confirmed MDH-CBD fusions (frozen from august)

16/09

Ran all the MDH-CBD fusions (prepared on 12/09)

17/09

Ran MDH assay again

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                        <li><a href="https://2015.igem.org/Team:Edinburgh/DNPBiosensor">DNP Biosensor</a></li>
                        <li><a href="https://2015.igem.org/Team:Edinburgh/PMABiosensor">PMA Biosensor</a></li>
                        <li><a href="https://2015.igem.org/Team:Edinburgh/CBD">Making it Stick</a></li>
-                       <li><a href="https://2015.igem.org/Team:Edinburgh/Results">Results</a></li>
+                       <li><a href="https://2015.igem.org/Team:Edinburgh/Results">Limits of Detection</a></li>
                      </ul>
                    </li>
@@ Line 45: / Line 45: @@
                      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Parts<span class="caret"></span></a>
                      <ul class="dropdown-menu" role="menu">
-                     <!-- <li><a href="https://2015.igem.org/Team:Edinburgh/Parts">Team Parts</a></li> -->
+                      <li><a href="https://2015.igem.org/Team:Edinburgh/Parts">Team Parts</a></li>
                        <li><a href="https://2015.igem.org/Team:Edinburgh/Basic_Part">Basic Parts</a></li>
                        <li><a href="https://2015.igem.org/Team:Edinburgh/Composite_Part">Composite Parts</a></li>
-                     <!-- <li><a href="https://2015.igem.org/Team:Edinburgh/Part_Collection">Part Collection</a> </li> -->
+                      <li><a href="https://2015.igem.org/Team:Edinburgh/Part_Collection">Part Collection</a> </li>
                        <li><a href="https://2015.igem.org/Team:Edinburgh/Improved_Part">Improved Parts</a></li>
                        <li><a href="https://2015.igem.org/Team:Edinburgh/Characterisation_Part">Improved Characterisation</a></li>
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                      </ul>
                    </li>
-                   <li><a href="https://2015.igem.org/Team:Edinburgh/MedalCriteria">Medal Criteria</a></li>
+                   <li><a href="https://2015.igem.org/Team:Edinburgh/MedalCriteria">Accomplishments</a></li>
              </ul>
          </div>
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 	<br>Miniprep cultures and nanodrop.
 <br>
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/6/6f/Edigem15_notebook_h13.png">
 <br>
 	<br>Diagnostic digest. No insert visible on gel.
@@ Line 309: / Line 309: @@
 	<br>Make glycerol stocks, miniprep and nanodrop cultures.
 <br>
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/5/5e/Edigem15_nb_h14.png">
 	<br>Diagnostic digest. Indicates the presence of insert.
 <br>
@@ Line 319: / Line 319: @@
 	<br>Make glycerols, miniprep and nanodrop cultures.
 <br>
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/e/e8/Edigem15_nb_h15.png">
 <br>
 	<br>Diagnostic digest.
@@ Line 341: / Line 341: @@
 	<br>Make glycerols, miniprep and nanodrop.
 <br>
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/7/78/Edigem15_nb_h16.png">
 <br>
@@ Line 352: / Line 352: @@
 	<br>Make glycerols, then miniprep and nanodrop cultures.
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/1/18/Edigem15_nb_h17.png">
 	<br>Diagnostic digest.
@@ Line 377: / Line 377: @@
 	<br>Make glycerols and miniprep cultures from 16/08. Nanodrop.
 <br>
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/7/79/Edigem18_nb_h18.png">
 <br>
 	<br>Diagnostic digest.
@@ Line 386: / Line 386: @@
 	<br>Amplify heroin esterase by PCR, PCR purify and nanodrop.
 <br>
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/8/86/Edigem15_nb_h19.png">
 <br>
 	<br>Diagnostic digest showed PCR amplified the correct sequence.
@@ Line 394: / Line 394: @@
 	<br>Make glycerols, miniprep and nanodrop cultures.
 <br>
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/a/a7/Edigem15_nb_h20.png">
 <br>
 	<br>Diagnostic Digest indicated the presence of insert in all but BBa_K863111 fusions.
 	<br>Amplify MorA by PCR, PCR purify and nanodrop.
 <br>
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/c/c7/Edigem15_nb_h21.png">
 	<br>Diagnostic digest showed PCR amplified the correct sequence.
 	<br>Inoculate successful transformants.
@@ Line 408: / Line 408: @@
 	<br>Make glycerols, miniprep and nanodrop cultures.
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/e/ee/Edigem15_nb_h22.png">
 	<br>Diagnostic digest indicated no insert was present.
@@ Line 428: / Line 428: @@
 	<br>Make glycerols and miniprep transformants from 20/08. Nanodrop.
 <br>
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/9/9a/Edigem15_nb_h24.png">
 <br>
 	<br>Diagnostic digest. Digest indicated the presence of inserts in some of the samples.
@@ Line 443: / Line 443: @@
 <br>
 	<br>Make glycerols of cultures, then miniprep and nanodrop.
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/2/2b/Ed15_nb_25.png">
 <br>
 	<br>Diagnostic digest indicated presence of insert in 1 fusion.
@@ Line 460: / Line 460: @@
 	<br>Make glycerols of cultures, miniprep and nanodrop.
 <br>
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/5/5e/Ed15_nb_26.png">
 <br>
 	<br>Diagnostic digest indicated the presence of insert in certain fusions.
@@ Line 484: / Line 484: @@
 	<br>Make glycerols of cultures, then miniprep and nanodrop.
 <br>
-	<br>TABLE IN HERE
+	<br><img src="https://static.igem.org/mediawiki/2015/8/83/Ed15_nb_27.png">
 	<br>Diagnostic digest showed insert was present in some fusions.
 <br>