Team:Newcastle/22 June 2010

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===QIagen Miniprep Kit Using a Microcentrifuge for Plasmid Extraction===
===QIagen Miniprep Kit Using a Microcentrifuge for Plasmid Extraction===
Please refer to: [[Team:Newcastle/Qiagen Minipreps|Qiagen Minipreps]] for materials required and protocol.
Please refer to: [[Team:Newcastle/Qiagen Minipreps|Qiagen Minipreps]] for materials required and protocol.
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===Digest===
===Digest===
Please refer to: [[Team:Newcastle/Restriction digests| Restriction digests]] for materials required and protocol.
Please refer to: [[Team:Newcastle/Restriction digests| Restriction digests]] for materials required and protocol.
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===Gel extraction===
===Gel extraction===
Please refer to: [[Team:Newcastle/Gel extraction| Gel extraction]] for materials required and protocol.
Please refer to: [[Team:Newcastle/Gel extraction| Gel extraction]] for materials required and protocol.
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===Agarose Gel Electrophoresis===
===Agarose Gel Electrophoresis===
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|[[Image:Newcastle_lab_1.jpeg|thumb]]
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|[[Image:Newcastle_lab_1.jpeg|thumb|Dr Wendy demostrating how to use gel electrophoresis machine]]
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|[[Image:Newcastle_lab_2.jpeg|thumb]]
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|[[Image:Newcastle_lab_2.jpeg|thumb|Gel tank]]
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|[[Image:Newcastle_lab_3.jpeg|thumb]]
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|[[Image:Newcastle_lab_3.jpeg|thumb|Deena pouring hot molten gel]]
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|[[Image:Newcastle_lab_4.jpeg|thumb|Putting the gel on the geldoc]]
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|[[Image:Newcastle_lab_5.jpeg|thumb]]
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|[[Image:Newcastle_lab_5.jpeg|thumb|Preparing to cut the gel]]
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|[[Image:Newcastle_lab_6.jpeg|thumb]]
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|[[Image:Newcastle_lab_6.jpeg|thumb|Gel illuminated by the UV light which is emitted by the geldoc]]
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We cut the inserts which were about 900bp and we use the backbone from the RFP plasmid.
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We cut the inserts which were about 900bp and we use the backbone from the plasmid consisting ''rfp''.
====QIAquick Gel extraction kit====
====QIAquick Gel extraction kit====
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|[[Image:Newcastle_lab_7.jpeg|thumb]]
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|[[Image:Newcastle_lab_7.jpeg|thumb|Phil cutting the gel]]
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|[[Image:Newcastle_lab_8.jpeg|thumb]]
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|[[Image:Newcastle_lab_8.jpeg|thumb|Transferring the cut gel part into a 2 ml microfuge tube]]
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The DNA fragments are cut from the agarose gel with a scalpel. Three parts of QG buffer is added to one part of gel and the mixtures are dissolved at the temperature of 50°C. The tubes are vortexed every 2-3 minutes to help dissolve the gel. 1 part of isopropanol is added to the sample and mix. The microcubes were spinned in the microfuge for 1 minute.
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==Set up ligation==
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====QIAquick gel extraction microcentrifuge protocol====
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# Excise the DNA fragment from the agarose gel with a clean, sharp scalpel
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# Weight the gel slice and add 3 volumes of buffer QG to 1 volume of gel (100 mg ~ 100 µl)
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# Incubate at 50°C and invert the tube gently at regular intrerval until the gel has completely dissolved
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# After the gel has dissovled completely, check that the color of the mixture is yellow
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# Add 1 gel volume of isopropanol to the sample and mix
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# Place a QIAquick spin column in a 2 ml collection tube
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# To bind DNA, apple the sample to the QIAquick column and centrifuge for 1 min
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# Discard the flow through and place the QIAquick column back into the same tube (Maximum volumn is 750ul)
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# Add 0.5 ml of Buffer QG to QIAquick column and centrifuge for 1 min and discard the flow through and place the QIAquick column back into the same tube
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# To wash, add 0.75 ml of Buffer PE to QIAquick column and centrifuge for 1 min and place the QIAquick column back into the same tube
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# Centrifuge the column for a further 1 min
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# Transfer the column into a clean 1.5 ml micriocentrifuge tube
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# To elute DNA, add 30 µl of Buffer EB to the center of the QIAquick membrane and allow to stand for 1 min
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# Centrifuge the column for 1 min and transfer the eluate to a clean 1.5 ml micriocentrifuge tube
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====Weighing====
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All gel extractions weighed 0.3g.
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===Set up ligation===
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===Transformation protocol===
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==Transformation protocol==
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# Thaw a 200µl aliquot of the desired strain of ''E. coli'' and add the transforming DNA (10 ng of vector DNA in 10 µl). Incubate for 45 min at 42°C.
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Please refer to: [[Team:Newcastle/Transformation of E. coli|Transformation of ''E. coli'']] for materials required and protocol.
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# Heat-shock the cells for 120 secs, and place on ice again for 3-4 min.
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# Add 1ml of LB broth and incubate the cells at 37°C for 1-15 hr in a water bath with gentle shaking.
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# Plate out 100-200 µl/plate on LB (agar at 1.5%), containing the appropriate selection markers.
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# Incubate plates overnight at 37°C.
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===Nanodrop Protocol===
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Nanodrop can be used to measure the DNA, RNA and protein
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# Select Nanodrop program from the desktop
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==Nanodrop Protocol==
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# To clean Nanodrop, add a drop of water on the spectrometer and press blank
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Please refer to: [[TeamNewcastleNanoDrop Spectrophotometer| Nanodrop Spectrophotometer]] for materials required and protocol.
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# After cleaning, wipe the water off
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# To equalizen the equipment, add 3 μl of the buffer used in the sample and press blank
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# Wipe the buffer off
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# To measure sample, add 3 μl of the sample and press measure
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# If dealing with multiple samples, clean the equipment with water at regular intervals
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# After measurement, clean the equipment with a drop of water on the spectrometer and press blank
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{|
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|[[Image:Newcastle_nanodrop_1.jpeg|thumb]]
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|[[Image:Newcastle_nanodrop_1.jpeg|thumb|A typical curve to be achieved from a nanodrop spectrophotmeter]]
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|[[Image:Newcastle_nanodrop_2.jpeg|thumb]]
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|[[Image:Newcastle_nanodrop_2.jpeg|thumb|Phil analyzing a sample on the nanodrop machine]]
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|[[Image:Newcastle_nanodrop_3.jpeg|thumb]]
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|[[Image:Newcastle_nanodrop_3.jpeg|thumb|Analyzed data on the screen]]
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Latest revision as of 20:42, 21 October 2010

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Contents

Aims

The aim of today's Lab practice was to extract the plasmids for GFP and RFP, digest the 2 plasmids and extract the 2 inserts and 1 of the backbones (vector)from an agarose gel. From this a ligation was set up.

Materials and Protocol

QIagen Miniprep Kit Using a Microcentrifuge for Plasmid Extraction

Please refer to: Qiagen Minipreps for materials required and protocol.

Digest

Please refer to: Restriction digests for materials required and protocol.

Gel extraction

Please refer to: Gel extraction for materials required and protocol.

Agarose Gel Electrophoresis

Please refer to: Gel electrophoresis for materials required and protocol.

Dr Wendy demostrating how to use gel electrophoresis machine
Gel tank
Deena pouring hot molten gel

Cut gel out

Putting the gel on the geldoc
Preparing to cut the gel
Gel illuminated by the UV light which is emitted by the geldoc

We cut the inserts which were about 900bp and we use the backbone from the plasmid consisting rfp.

QIAquick Gel extraction kit

Phil cutting the gel
Transferring the cut gel part into a 2 ml microfuge tube

Set up ligation

Reagents 1:3(μl) 1:5(μl) Vector(μl)
V 0.8 0.8 1
G 2.7 4
R 5.4 7.7
LT4 1 1 1
LB 1.1 1.5 1
H2O 0 0 7
Total Volume 11.0 15.0 10.0

Transformation protocol

Please refer to: Transformation of E. coli for materials required and protocol.

Nanodrop Protocol

Please refer to: Nanodrop Spectrophotometer for materials required and protocol.


A typical curve to be achieved from a nanodrop spectrophotmeter
Phil analyzing a sample on the nanodrop machine
Analyzed data on the screen

Outcome

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