But they all consist of 4 nucleotides 2 made of purine bases which are adenine and guanine and 2 pyrimidine bases which are thymine and cytosine. The purine based nucleotides always pair with their base pair pyrimidine based nucleotide.In DNA Adenine is paired with thymine and guanine pairs with cytosine.But if it's RNA there is a special exception which replaces thymine with Uracil pairing with adenine.he purine based nucleotides always pair with their base pair pyrimidine based nucleotide. In DNA Adenine is paired with thymine and guanine pairs with cytosine.