I am new in molecular biology and do not have enough educational background. I try to learn and understand PCR steps. I have questions about primer design.( And I study for a lab where diagnosis of plant viruses were done)
When I look over the sci. papers, the primers were designed to target the coat protein conserved regions of the viruses. As far as I know, conserved sequences are similar sequences that occur within nucleic acid sequences across species or within different molecules produced by the same organism. As I understand a conserved regions can locate in two closely related viruses. For instance, Potato virus A, Potato virus Y.
When I use NCBI conserved region domain for Y and A
GenBANK says coat protein gene is conserved region both PVY and PVA. So I should design my primers in coat protein gene region?
If I do, could it be logical, because they both potyvirus and can share same nucleotide.
But the papers I looked always use primers that were designed to target the coat protein gene of viruses.
I am confused. Can anyone help?