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Can a primer bind to DNA in a 5'-3 parallel fashion? - Just wondering... (May/20/2010 )

Hey guys,

Someone put forward this question to me today:

If I have a primer (5'-3'), can it bind to a complementary DNA sequence (5'-3' also)?

Sort of like (example only, yeah)


I guess. Is this scenario possible?

If it binds, can this pairing be amplified in PCR?
What do you guys think?



Binding is always in the oposite orientation of strands.

So like this in this case:


That means it's not complementary except for some weak 2-3bp interactions.

Check it with IDT Oligo Analyser.