Difference Between Cross Homology and Cross Dimer In A PCR Primer

AnushaC · 05-16-2016, 05:07 PM

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 · 05-16-2016, 08:53 PM

You will find definitions and more in the following link:
http://www.premierbiosoft.com/tech_n...er_Design.html

AnushaC · 05-16-2016, 10:38 PM

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 · 05-16-2016, 11:27 PM

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.

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05-16-2016, 05:07 PM	#1
AnushaC Member Location: San Diego Join Date: Sep 2013 Posts: 78	Difference Between Cross Homology and Cross Dimer In A PCR Primer 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

05-16-2016, 08:53 PM	#2
nucacidhunter Jafar Jabbari Location: Melbourne Join Date: Jan 2013 Posts: 1,238	You will find definitions and more in the following link: http://www.premierbiosoft.com/tech_n...er_Design.html

05-16-2016, 10:38 PM	#3
AnushaC Member Location: San Diego Join Date: Sep 2013 Posts: 78	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

05-16-2016, 11:27 PM	#4
nucacidhunter Jafar Jabbari Location: Melbourne Join Date: Jan 2013 Posts: 1,238	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.