First question is about why we use primers in PCR. It requires two reasons. I know only one reason though. It is so that DNA polymerase can attach to primer and make a copy of nucleotide from there. But i don't know what is the other reason. Another question is about why the primer bonds to 3' end of the DNA you want to copy. and explained why. I really have no clue for this one. Plzz help.
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2$\begingroup$ "why the primer bonds to 3' end of the DNA you want to copy. and explained why. I really have no clue for this one." How did you get to learning about PCR and not learn that DNA is antiparallel? DNA always has a polarity. Single stranded DNA has a 5' to 3' polarity. So do primers, which are just short ssDNAs. $\endgroup$– AMRCommented Oct 13, 2015 at 2:31
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3 Answers
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We use primers in PCR because we are mimicing natural processes. DNA polymerase cannot act without primers. It needs primers to start it's work. Binding of molecules happen by chance, so the more there are of your primer, the more likely it is that it would bind to any given string of complementary DNA. DNA replication occurs in the five prime to three prime direction because phosphate doesn't allow the reverse reaction.
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When a new nucleotide is added on to a growing DNA molecule, the reaction takes place on the hydroxyl group at the 3' end. The 5' end is a phosphate group, so it can't add there. It always has to add to the OH at the 3' end, so we say DNA always grows from 5' to 3'. Alcohols are fairly reactive and are intermediates in a number of reactions, if that helps you to remember.
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Beside helping Taq to add dntps to the growing strand Primers minimize the risk of mishybirdization as they are designed specifically for a specific region of DNA
