Hoogsteen base pair

A Hoogsteen base pair is a variation of base-pairing in nucleic acids such as the A•T pair. In this manner, two nucleobases, one on each strand, can be held together by hydrogen bonds in the major groove. Specifically, it happens when a pyrimidine base (C/T) uses its Watson–Crick (anti, N3–C4) face to bind the syn (N6–N7) face of a purine (A/G).

Adenine, which is not a pyrimidine, is capable of using its anti (N1–N6) face to pair with the syn face of a purine to form a Hoogsteen-like base pair. Guanine can form a similar interaction with another purine base, forming a rigid cycle called a guanine tetrad in the case of four guanines. These are also "Hoogsteen base pairs" under the expanded understanding as anti-syn interaction.

A reverse Hoogsteen base pair is when a pyrimidine's syn (N3–C2) face binds a purine's syn face. Under a systemic view of non-canonical base pairing, Hoogsteen base pairs (in the expanded sense) are called Watson-Crick/Hoogsteen, based on what faces are interacting (the syn face is called the Hoogsteen face). The reverse Hoogsteen base pair is called "Hoogsteen/Hoogsteen".

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