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A question regarding PCR

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A question regarding PCR

Postby x555 » Sat Jan 18, 2014 11:05 am

Hello everyone. Let's say I have this microsatellite DNA sequence:

5’-acatttg CTT CGTACACAAC TGTGCGAACA TGC caacctca tgcaacctca
cacacacaca cacacacaca cacacacaca cacacacaca cacacacaca cacacacaca cacacacaca cacacacaca cacacacaca cacacacaca cacacacaca cacacattcg
acggttgcag GCAAATACTG CCCTGTGGGG-3’

The places where primers should attach are written in capitals. My question is how many base pairs the amplified product will have, but it's not clear to me how to answer it. When the two DNA strand separate and have polymerases amplifying them, won't the initial products have different lengths since there is this little acatttg sequence before the first primer position? I mean, won't the product of the 5'-3' strand be 7 base pairs longer than the product of the 3'-5' strand?
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Postby JackBean » Sat Jan 18, 2014 2:36 pm

probably, your microsatellite is part of the chromosome, right? So there will be much more than 7 bp and it will be on both sides.

Yes, the polymerase will amplify the chain until the conditions change (i.e. end of amplification step) or until it falls off (which may happen with very long amplicons, that's why you need special polymerase for PCR of long pieces). However, this long (of ununiform length) amplicons will increase in number only lineary, while the amplicon of desired length will increase exponentially, because from every longer-than-should-be amplicon only the amplicon of right size will rise.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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