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# Optimal target length

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### #1 The Question

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Posted 17 November 2009 - 09:19 AM

Hi everybody

I'm new for qPCR and was wondering what can be the optimal target length in qPCR.
One month before I was using primers for target length of 250 and now I'm using the primers for the target length of 60. Can bad target length be problem to determine melting temperature? And can it cause any other problems?

We can find answers following our own ideas.

### #2 ciyiben

ciyiben

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Posted 19 November 2009 - 09:45 AM

Hi

In theory, an optimal lenght would be between 100 and 200.

Good luck

### #3 The Question

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Posted 20 November 2009 - 03:43 AM

ciyiben, on Nov 19 2009, 06:45 PM, said:

Hi

In theory, an optimal lenght would be between 100 and 200.

Good luck

Thanks for reply. Now I've question what can be the problem of shorter target like 60 nucleotides in length, which I'm using.
We can find answers following our own ideas.

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Posted 23 November 2009 - 01:47 PM

Imagine you need to amplify between 200-400bp after your quantification.
If your DNA is degraded, a 60bp qPCR may give you an overestimation of what you have in your tube.
There might be a lot of 60bp fragments but far less 400bp fragments.
When the DNA is pristine, it usually isn't a problem. This is why AB developed Quantifiler with a 62bp amplicon.

To sumarize, I'd try to use a size as close as possible as the the size of the amplicon you will target (unless it's huge of course).

Hope this helps.
Theory is when we know everything and nothing is working. Practice is when everything is working and nobody knows why. Here, we combine theory and practice. Nothing is working and nobody knows why.

A. Einstein