Microarrays, RNAseq And Functional Genomics CPSC265 Matt Hudson.
Colony PCR CPSC265 Class 8. Cloning Cloning is the way in which we can take a single molecule, and...
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Transcript of Colony PCR CPSC265 Class 8. Cloning Cloning is the way in which we can take a single molecule, and...
![Page 1: Colony PCR CPSC265 Class 8. Cloning Cloning is the way in which we can take a single molecule, and make lots of bacterial cells that contain an identical.](https://reader036.fdocuments.net/reader036/viewer/2022072006/56649cfd5503460f949cddce/html5/thumbnails/1.jpg)
Colony PCR
CPSC265 Class 8
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Cloning
• Cloning is the way in which we can take a single molecule, and make lots of bacterial cells that contain an identical molecule.
• These cells are clones, hence the name
• This used to be the only way to amplify DNA. It is still by far the most accurate.
![Page 3: Colony PCR CPSC265 Class 8. Cloning Cloning is the way in which we can take a single molecule, and make lots of bacterial cells that contain an identical.](https://reader036.fdocuments.net/reader036/viewer/2022072006/56649cfd5503460f949cddce/html5/thumbnails/3.jpg)
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Plasmid vectors – circular, autonomous bacterial DNA
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The vector is made with a “T” overhang
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Taq polymerase leaves an “A” overhang
• Taq is the thermostable DNA polymerase from Thermus aquaticus we used for PCR.
• When Taq synthesizes a new strand, it always puts an extra “A” at the end
• This can be useful, but note: other polymerases do not do this, they leave “blunt” ends. Only Taq polymerase leaves ‘A’ overhangs. ‘Blunt’ end vectors do not work with Taq, we need a ‘T’ overhang.
![Page 7: Colony PCR CPSC265 Class 8. Cloning Cloning is the way in which we can take a single molecule, and make lots of bacterial cells that contain an identical.](https://reader036.fdocuments.net/reader036/viewer/2022072006/56649cfd5503460f949cddce/html5/thumbnails/7.jpg)
![Page 8: Colony PCR CPSC265 Class 8. Cloning Cloning is the way in which we can take a single molecule, and make lots of bacterial cells that contain an identical.](https://reader036.fdocuments.net/reader036/viewer/2022072006/56649cfd5503460f949cddce/html5/thumbnails/8.jpg)
DNA ligase
• Repairs gaps in the sugar-phosphate backbone of DNA
• Creates phosphodiester bonds
• Does not do anything with the bases
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Transformation of bacteria
• Two main methods for transformation
• Chemical / Heat Shock
As done in last practical, this method gets DNA into the cell by making them porous using CaCl2 and a 42 C heat treatment
• Electroporation
Makes cells porous using high-voltage electricity
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Imperfect science
• Most of the plasmid / insert combinations will not ligate
• Most of the bacteria will not be transformed
• We only need one molecule to get into one bacterium to make one colony.
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PCR from clones
• Often clones will religate containing any old DNA (eg primer dimers)..
• The DNA can go in in either orientation
• We can use the PCR to tell which colonies have the insert we want, and which orientation it is in.