Competition between binding DNA in qPCR

[YoBie]

In a PCR after the denaturation step (forming single stranded DNA), DNA will have to possiblilty to bind it's own's nucleotides to it's own strain, forming hairpins. These loops could interfere with primers

Now my mentor told me that the binding of primers and hairpins have a competitive behaviour.

Can somebody explain this to me?
My thoughts are that the energy needed for the bindings are in favor for the primers for binding than for the own DNA, since bending the DNA will also costs energy.

[MEDIBENA]

Originally Posted by YoBie

In a PCR after the denaturation step (forming single stranded DNA), DNA will have to possiblilty to bind it's own's nucleotides to it's own strain, forming hairpins. These loops could interfere with primers

Now my mentor told me that the binding of primers and hairpins have a competitive behaviour.

Can somebody explain this to me?
My thoughts are that the energy needed for the bindings are in favor for the primers for binding than for the own DNA, since bending the DNA will also costs energy.

your mentor is right that the hairpins have a competetive behaviour to your primer, but you shoud think about it once you design the primers. what i usualy do i blast the primer i design with the known sequence to search for homology within the organismus i am working with. If there is match i try to redesign primers to increase specificty by increasing basepares or locate the primers at the different place with litle or no homology in the genom.