Difference Between Cross Homology and Cross Dimer In A PCR Primer

[AnushaC]

Dear All,

What is the difference between cross homology and cross dimer in a PCR primer and can you give one example of each of those.



Thanks,
Anusha

[nucacidhunter]

You will find definitions and more in the following link:

http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html

[AnushaC]

Hi,

I did read the link you mentioned which gives an example of cross dimer

iii) Cross Dimer: Primer cross dimers are formed by intermolecular interaction between sense and antisense primers, where they are homologous. Optimally a 3' end cross dimer with a ΔG of -5 kcal/mol and an internal cross dimer with a ΔG of -6 kcal/mol is tolerated generally.
Cross Dimer

But gives no explanation of cross homology , nor any example justifying why it is a cross-homologous primer

[nucacidhunter]

Another name for cross dimer is primer-dimer.

“11. Avoid Cross Homology: To improve specificity of the primers it is necessary to avoid regions of homology. Primers designed for a sequence must not amplify other genes in the mixture. Commonly, primers are designed and then BLASTed to test the specificity.”

Basically it refers to specificity of primer. Most primers will amplify non-target regions if there is enough homology in 3’ region under submissive conditions.