Team:Exeter/lab book/3gip/wk3

Operon Construction  |  Glycobase

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Monday 23rd July

Morning

•Preparation of IDTE buffer

Protocol was followed exactly.

Tuesday 24th July

Morning

•3A Assembly

BBa_K206001 + BBa_B0034

BBa_K206000 + BBa_B0034

BBa_K094120 + BBa_B0034.

Afternoon

• IDT resuspension and transformation of wbnJ and wfcA

Alex and Becca finished the transformation of the wbnJ and wfcA genes while Mary and I continued with the BioBrick transformation.

2ul of DNA was used for each transformation into Invitrogen TOP10 competent cells using the protocol provided.

Tuesday 25th July

Morning

The 3A assembly and subsequent transformation performed on Tuesday 24th July showed no colonies in the morning. It was thought the problem may be that the BBa_B0034 sequence was too small (12bp). We decided to run the 3A assembly again but this time alongside the standard assembly allowing us to compare.

•3A Assembly

The 3A assembly was repeated for:

BBa_K206000 + BBa_B0034 into pSB1T3

BBa_K094120 + BBa_B0034 into pSB1T3

• Standard assembly

Standard assembly using BBa_B0034 in the destination plasmid. The amount of DNA used was increased to 2000ng and the total H20 was changed from 50μl to 35μl to fit the gel.

For the standard assembly the samples were digested for 1 hour at 37°C.

A 50μl 8% gel, using low melting agarose, was prepared.

While the gel was drying we used a Qiagen Purification Kit to purify the downstream BBa_B0034 digestion. This was performed using the Qiagen Gel Extraction Protocol exactly.

Afternoon

• Standard assembly Gel Purification

The digested upstream DNA, BBa_K206000 and BBa_K094120, were run on the 8% gel. The gel was run for 20 minutes until the dye had run 2 thirds the length of the gel.

The gel was taken into the darkroom, visors were worn and lab coats tucked into gloves. The UV tray was pulled out and turned to low. BBa_K206000 and BBa_K094120 showed faint bands but after attempting to cut them out, it was decided that not enough DNA was present for gel purification.

•Transformation

Products of the 3A assembly:

BBa_K206000 + BBa_B0034

BBa_K094120 + BBa_B0034

Using Invitrogen TOP10 competent cells split between 2 eppendorfs so that each contained 25μl

Spread on two tetracycline plates for each transformation using 20μl and 100μls respectively.

Wednesday 26th July

Afternoon

•Transformation

Pbad promoter BBa_I0500, 2012 Distribution Kit Plate 1, 14N

•Transferring colonies to liquid medium

Cells containing BBa_K206000 + BBa_B0034 and BBa_K094120 + BBa_B0034 both showed colonies and were added into liquid medium and incubated overnight

Protocol was followed using kanamycin for all BioBrick parts as the selection antibiotic.

Thursday 27th July

Morning

Pbad promoter BBa_I0500 showed colonies and was stored in the fridge until Monday.

•Miniprepping

BBa_K206000_BBa_B0034

BBa_K094120_ BBa_B0034

Both BBa_K206000_BBa_B0034 and BBa_K094120_ BBa_B0034 were nanodropped and recorded good concentrations.

•Gel Electrophoresis

Run to check fragment sizes of BBa_K206000_BBa_B0034 and

BBa_K094120_ BBa_B0034 after digestion using the EcoR1 and Pst1 enzymes

Gel Electrophoresis showed no bands but this may have been down to the small size of the inserts.

Streak plates were made from the overnight cultures and left on the bench until Monday.