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Can a primer bind to DNA in a 5'-3 parallel fashion?


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#1 chrisbelle

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Posted 20 May 2010 - 12:24 AM

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)

5'-AGCTTGCTGAGTGC-3'
5'-AACGACT-3'

I guess. Is this scenario possible?

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

Chris
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#2 Trof

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Posted 20 May 2010 - 03:57 AM

Binding is always in the oposite orientation of strands.

So like this in this case:

5'-AGCTTGCTGAGTGC-3'
3'-TCAGCAA-5'

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

Check it with IDT Oligo Analyser.

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