Team:TU Delft/17 August 2010 content

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Revision as of 14:00, 18 August 2010

Alkane degradation

Digestion

Yesterday's transformed competent cells of the 014C, 020C, 405C, 327C and 304C ligation mixes (using the BioBrick assembly method) yielded only red colonies, indicating the lack of positive colonies. It is interesting to note the presence of numerous red colonies on the digest control plate, whereas the ligation control plate (Digested pSB1C3 + ligase buffer + ligase) yielded but 1 red colony (at similar trasnsformation mix concentrations). Based on the information gathered thus far a few hypotheses were made:

Hypothesis I: The ligase buffer inhibits transformation efficiency in some way.

Hypothesis II: The ligation time of 20 mins was too short.

In order to test hypothesis I, the following mixes will be transformed into commercial competent cells:

#	Fragment 1	Ligase buffer?	Total volume (uL)
1	E-pSB1C3-P (2 uL)	No	20
2	E-pSB1C3-P (2 uL)	Yes (2 uL)	20

In order to test hypothesis II, a ligation kinetics assay was performed using E and P digested pSB1C3 as vector and J04450 as insert. The ligations were run for 30, 60, 120 and 240 minutes.

Furthermore, a second attempt was made at creating BioBricks 014C, 020C, 405C, 327C and 304C. pSB1C3 was digested additionaly using HindIII to cut the J04450 insert as follows:

#	Sample	Enzyme 1	Enzyme 2	Enzyme 3	Buffer	BSA	Needed fragment
1	pSB1C3	EcoRI	PstI	HindIII	NEBuffer 3	✓	‘E - pSB1C3 - P’

The digestion mix was incubated at 37 degrees for 1 hour and at 80 degrees for 20 minutes to inactivate the restriction enzymes. The mixes were checked on 1% agarose gel:

1% agarose gel run at 90V for 50 min. Of all samples 10 µL was loaded with 2 µL loadingbuffer. 2 µL was loaded of marker

Lane description

#	Description	Expected size (bp)	OK?
1	Smartladder	Varies	Yes
2	pSB1C3 E+P digest	2035, 1081	Yes
3	pSB1C3 E+P+HindIII digest	2035, 456, 403, 222	Yes

From the gel it could be concluded that the digestions were succesful.

Ligation

Following the digestion the products were ligated for 4 hours at 20 degrees and the ligase inactivated at 80 degrees for 20 min.:

#	BioBrick	Fragment 1	Fragment 2	Destination Vector
1	014C	‘E - J23100-X-J61100-alkB2-J61100-rubA3 - S’	‘X - J61100-rubA4-J61100-rubR-B0015 - P’	‘E - pSB1C3 - P’
2	020C	‘E - J23100-X-J61100-ladA - S’	‘X - J61101-ADH - P’	‘E - pSB1C3 - P’
3	405C	‘E - J23100-X-J61101-PhPFDα - S’	‘X - J61101-PhPFDβ - P’	‘E - pSB1C3 - P’
4	327C	‘E - pCaiF - S’	‘X - B0032 - P’	‘E - pSB1C3 - P’
5	304C	‘E - pAlkS - S’	‘X - B0032 - P’	‘E - pSB1C3 - P’
6	Ligation control	None	None	‘E - pSB1C3 - P’

To test whether the ligations were succesful, 1 uL of ligation mix was used as template for a PCR amplification.

@@ Line 78: / Line 78: @@
 |}
-From the gel it could be concluded that the digestion were succesful.
+From the gel it could be concluded that the digestions were succesful.
 ====Ligation====
-Following the digestion the products were [[Team:TU_Delft/protocols/ligation|ligated]] for 15 minutes at RT:
+Following the digestion the products were [[Team:TU_Delft/protocols/ligation|ligated]] for 4 hours at 20 degrees and the ligase inactivated at 80 degrees for 20 min.:
 {| style="color:black; background-color:white;" cellpadding="5" cellspacing="0" border="1"
@@ Line 128: / Line 126: @@
 |None
 |‘E - pSB1C3 - P’
-|-
-|7
-|014C
-|‘E - J23100-X-J61100-alkB2-J61100-rubA3 - S’
-|‘X - J61100-rubA4-J61100-rubR-B0015 - P’
-|‘E - pSB1C3 - P’ (Pre-shipped linearized plasmid)
 |}
-The ligations were performed in parallel: one batch using the NEB T4 DNA ligase and buffer, the other batch the Fermentas T4 DNA ligase and buffer. We hope to be able to discern the differences in efficiency between the two (if there are any).
+To test whether the ligations were succesful, 1 uL of ligation mix was used as template for a PCR amplification.
-To test whether the ligations were succesful, i uL of ligation mix was used as template for a PCR amplification. The results will be known by tomorrow.