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MSP primers- finding the product length


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#1 jezwilliamson

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Posted 30 July 2012 - 04:43 AM

Hi,


I've found some MSP primers for the MINT1 gene which have been used by most of the studies i've found on pubmed related to my research, however, none of the papers quote the product length. I've pretty much looked at all the papers which quote these primers.

Is there an easy way to find out the product length if you know the primer sequences?

Cheers!!

#2 pcrman

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Posted 30 July 2012 - 10:54 PM

The easiest way for you to find the amplicon size is to obtain the genomic sequence for MINT1 gene including its promoter, do a virtual bisulfite conversion (change all CpG "C"s to T), and use the converted sequence to search for the primers. If you are luck enough (the original authors did the right design, and listed the right sequences), you can find the primers in the sequence and the amplicon size. You may also try a tool called BiSearch to search the primers against bisulfite converted genome.

#3 gfischer

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Posted 31 July 2012 - 01:40 PM

A free in silico PCR utility can be found here: http://genome.ucsc.e...r?command=start
Just select the species of interest, insert the primers and you should get a readout of predicted amplicons with length.
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then heaven will be yours, before you meet your end

#4 pcrman

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Posted 31 July 2012 - 02:37 PM

In this case, UCSC in silico PCR tool cannot help because the primers are designed on buslfite converted DNA.

#5 gfischer

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Posted 01 August 2012 - 06:13 AM

Ah yes, my mistake.

Carry on then.
Above all things, if kindness is your king,
then heaven will be yours, before you meet your end




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