The key difference between Watson and Crick and Hoogsteen base pairing is that Watson and Crick’s base pairing is the standard way that describes the formation of base pairs between purines and pyrimidines. Meanwhile, Hoogsteen base pairing is an alternative way of forming base pairs in which the purine takes a different conformation with respect to pyrimidine.
A nucleotide has three components: a nitrogenous base, a pentose sugar and a phosphate group. There are five different nitrogenous bases and two pentose sugars involved in the structure of DNA and RNA. When these nucleotides form a nucleotide sequence, complementary bases, either purines or pyrimidines, form hydrogen bonds between them. This is known as base pairing. Therefore, a base pair is formed by joining two nitrogenous bases by hydrogen bonds. Watson and Crick’s base pairing is the classic or standard approach, while Hoogsteen base pairing is an alternative way of forming base pairs.
