I was making primers for Polymerase Chain Reaction, when i was told to add sitting site for the polymerase, but couldn't find a definition of sitting sequence, or the reason of adding the same.
I have not heard of a sitting site for polymerases in pcr but when you are cutting the pcr product with restriction enzymes for cloning many enzymes need not only the cut site on the 5' end of the primer but also afew random bases extra that allows the restriction enzyme to sit on the dna and allow cutting. NEB have a link showing how many extra bases each enzyme needs
Adding a polymerase "sitting site" or "sitting sequence" to primers is usually necessary when you're working with a polymerase that requires a bit of extra DNA to latch onto before it can start amplifying your target sequence. This is particularly common when you're using primers designed to add extra sequences, like restriction enzyme sites, overhangs, or tags, to the ends of your PCR product.
Polymerases, especially ones like Taq, need a stable platform (typically 4–6 extra nucleotides) upstream of the target sequence for efficient binding and extension. Without these extra bases, the polymerase might struggle to attach properly, which can lead to inefficient amplification or failed PCR.
So, if your primers include additional sequences for downstream cloning or labeling, make sure to add a few extra nucleotides at the 5' end to give the polymerase a "place to sit." It's not part of the target sequence but ensures your experiment works smoothly.
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