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migue migue
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11 years ago
I have inserted a DNA sequence into a plasmid (pET vector) and now have to check the recombinant plasmid has the desired gene sequence. I've been told the primer sequence for this must be upstream from the region I wish to check - do I use a primer that has a sequence complementary to the sequence I wish to check?? If so how does it bind to the DNA upstream?? And does it have anything specific attached to the ends of the primer??
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wrote...
11 years ago
so what you want to do know is "screen" your colonies

so im assuming you have some colonies growing on an agar plate, right? set up a pcr where you can screen lets say at least 10 of those colonies. im assuming you know how to set that up...then just use a sterile tip or anything really (of course sterile) to pick up a tiny bit of the colony and add it directly into the pcr mixture (this = your template). each time you pick a colony either circle that colony on your plate, or streak it onto a defined section of another agar plate (so that when you know which ones contain the gene, you have a tiny stock of them ready of whatever you want to do with them)

yes youd need both a forward and reverse primer, not directly "on" your sequence, ie. slightly up or down stream of it. using a computer program that displays your sequence and the binding site of your primers, you can figure out the expect number of base pairs that will be amplified by PCR...run your pcr products on a gel and look to see which colonies show a band of the expected size. its good that you know what vector you're dealing with was the primer sequences will likely contain (be complimentary to) some of the plasmid sequence

p.s. when you run the gel it is actually a good thing if you see some that some colonies contain the insert, and see some that dont. it would just be too sketchy if everything worked perfectly..
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