I am new to molecular biology and unfortunately I don't understand the primer design process.
I need to carry out PCR prior direct sequencing, for example. I know there are several programs that design primers like Primer3, Primer express. I have to paste the DNA sequence, right? But I don't need the whole DNA, I only need one exon to be genotyped later, so what should I do? Should I paste the sequence of this exon only? or should I copy a part of gene DNA that is a little bit longer (both sides) than my exon? however, an intron goes after the exon I need, so should I copy the mRNA sequence in this case?
My second question is how can I design a sequencing primer? can I use a forward primer already designed for PCR?
I know the questions are very simple and may even be stupid, but I just don't get it
I would be very grateful for your answers