From MSP primer to gene - how to recalculate original DNA sequence? (Sep/07/2005 )
From the literature, I have 2 primer sets which are used for methylation specific PCR (specific for unmethylated (U) or methylated (M) DNA).
I'm trying to find the complementairy sequence in the gene, but I'm getteing completely confused. Is it possible to re-calculate the original sequence in the gene from the primer sequense?
The primer sequence are the following:
UF 5'-TAGGATTTGTTTTGTGTATG-3'
UR 5'-ACCACATCACCCATTAACCACA-3'
MF 5'-TAGGATTCGTTTCGCGTACG-3'
MR 5'-ACCGCGTCGCCCATTAACCGCG-3'
See the attachement for the same sequences, now with putative methylation sites in bold.
Thanks for your help
it's possible if you know which bases within the primer are conversion events.
from you doc file it's really difficult to determine as there are a string of bold sequences where you would not expect methylation and/or conversion!!
If you want to map the primer back to the original DNA sequence, you can paste the DNA sequence into word or a text processing program, replace all non-cpg Cs with T, then search for the primer sequence in the converted DNA sequence. If you have some sequence processing program such as NIT vector, DNA star, it is much easier to look up.
from you doc file it's really difficult to determine as there are a string of bold sequences where you would not expect methylation and/or conversion!!
Yes, that's exactly the problem I was having...
Thanks!
I found the binding sites for the primers.