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Revision as of 11:08, 27 July 2007 (view source) David.bikard (Talk | contribs) (→Oligo design for Wanner deletion) ← Older edit		Revision as of 16:34, 27 July 2007 (view source) David.bikard (Talk | contribs) Newer edit →
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	*dFtsZ-R		*dFtsZ-R
	GAAACCCAAATTCCAGTCAATTCTTAATCAGCTTGCTTACGCAGGAATGCTGTAGGCTGGAGCTGCTTCG  (P6 + P2)		GAAACCCAAATTCCAGTCAATTCTTAATCAGCTTGCTTACGCAGGAATGCTGTAGGCTGGAGCTGCTTCG  (P6 + P2)
		+
		+
		+	== Ligations ==
		+	{|
		+	|- style="background: #ccccff;"
		+	! colspan="5" style="background: #ccccff;" | Ligations
		+	|- style="background: #ccccff; text-align: center;"
		+	|width=5%| Number
		+	|width=25%| Insert
		+	|width=5%| Insert Volume (µL)
		+	|width=25%| Vector
		+	|width=5%| Vector Volume (µL)
		+	|width=35%| Comments
		+	|- style="background: #cccccc;"
		+	| style="background: #ccffcc;" |L1
		+	|D23.1 (AraC/pBad promoter FI)
		+	|8.5
		+	|D9.1 (J61002 ready for insertion of a FI)
		+	|1.5
		+	|construct with pBad promotor regulating expression of mRFP (in order to test activity of pBad)
		+	|- style="background: #cccccc;"
		+	| style="background: #ccffcc;" |L6
		+	|D14.1 (Cre ORF)
		+	|8
		+	|D15.1 (B0030 BV)
		+	|2
		+	|construction of the biobrick strong RBS(B0030)-Cre ORF
		+	|- style="background: #cccccc;"
		+	| style="background: #ccffcc;" |L9
		+	|lox66 [O14+O15] (0.2µM)
		+	|2
		+	|D22.1 (pSB1A2 Eco, Pst)
		+	|2 (+6 H2O)
		+	|lox66 cloned as a biobrick in pSB1A2
		+	|- style="background: #cccccc;"
		+	| style="background: #ccffcc;" |L10
		+	|lox71 [O16+O17] (0.2µM)
		+	|2
		+	|D22.1 (pSB1A2 Eco, Pst)
		+	|2 (+6 H2O)
		+	|lox71 cloned as a biobrick
		+	|}

---

Revision as of 16:34, 27 July 2007

Contents 1 PCR to perform 2 Oligo design for Wanner deletion 2.1 DapA deletion 2.2 FtsZ deletion 3 Ligations

PCR to perform

Perform the following PCR reactions

• P5 (then perform digestion rxn D18 & D20)
• P6 (then perform digestion reactions D19 & D21)
• P8
• P9

Repeat ligation reactions (same as 25/07/07). Also include digestion products D28 & D32

Oligo design for Wanner deletion

We were for now on not able to perform the deletion of DapA through transduction. So we will try the deletion through the Wanner method. We will also attempt the deletion of FtsZ.

We will use the protocol of the keio collection: [http://ecoli.naist.jp/gb6/Resources/deletion/Del_construct.html]

• 20nt of upstream region of kan gene,

5'-ATTCCGGGGATCCGTCGACC-3' (P1)

• 20nt of kan downstream sequence,

5'-TGTAGGCTGGAGCTGCTTCG-3' (P2)

DapA deletion

• 50nt DapA upstream region

5'-CATACCAAACGTACCATTGAGACACTTGTTTGCACAGAGGATGGCCCATG-3' (P3)

• 50nt DapA downstream region (reverse complement)

5'-AAGCCATCAAATCTCCCTAAACTTTACAGCAAACCGGCATGCTTAAGCGC-3' (P4)

• dDapA-F

CATACCAAACGTACCATTGAGACACTTGTTTGCACAGAGGATGGCCCATGATTCCGGGGATCCGTCGACC (P3 + P1)

• dDapA-R

AAGCCATCAAATCTCCCTAAACTTTACAGCAAACCGGCATGCTTAAGCGCTGTAGGCTGGAGCTGCTTCG (P6 + P2)

FtsZ deletion

• 50nt FtsZ upstream region

5'-GACGATGATTACGGCCTCAGGCGACAGGCACAAATCGGAGAGAAACTATG-3' (P5)

• 50nt FtsZ downstream region (reverse complement)

5'-GAAACCCAAATTCCAGTCAATTCTTAATCAGCTTGCTTACGCAGGAATGC-3' (P6)

• dFtsZ-F

GACGATGATTACGGCCTCAGGCGACAGGCACAAATCGGAGAGAAACTATGATTCCGGGGATCCGTCGACC (P5 + P1)

• dFtsZ-R

GAAACCCAAATTCCAGTCAATTCTTAATCAGCTTGCTTACGCAGGAATGCTGTAGGCTGGAGCTGCTTCG (P6 + P2)

Ligations

Ligations
Number	Insert	Insert Volume (µL)	Vector	Vector Volume (µL)	Comments
L1	D23.1 (AraC/pBad promoter FI)	8.5	D9.1 (J61002 ready for insertion of a FI)	1.5	construct with pBad promotor regulating expression of mRFP (in order to test activity of pBad)
L6	D14.1 (Cre ORF)	8	D15.1 (B0030 BV)	2	construction of the biobrick strong RBS(B0030)-Cre ORF
L9	lox66 [O14+O15] (0.2µM)	2	D22.1 (pSB1A2 Eco, Pst)	2 (+6 H2O)	lox66 cloned as a biobrick in pSB1A2
L10	lox71 [O16+O17] (0.2µM)	2	D22.1 (pSB1A2 Eco, Pst)	2 (+6 H2O)	lox71 cloned as a biobrick