Different sized product for same BS primer!
Posted 03 June 2010 - 07:11 AM
Im going to send them for sequencing, but any ideas meanwhile!!!??
Posted 03 June 2010 - 04:47 PM
As a control, i also the use the same primer set on genomic DNA to ensure there is no nonspecific binding
How can you use the same primers to amplify genomic DNA (DNA w/o modification)? But it is a good idea to design a new set of genomic PCR primers (on unmodified DNA) to verify that BSP primers did not amplify the smaller amplicon by non-specific priming which is easier with modified DNA.
Posted 04 June 2010 - 12:11 AM
So for the second set, I ran the genomic DNA control to make sure I wasnt picking up anything from unconverted DNA which will form part of the population in my bisulphite treated sample. Once this was clean, I proceeded to test all my different tissues (with now different sized amplicons.)
I will follow your suggestion and check my amplicons sizes again! THanks a lot!