Hoogsteen base pair

A Hoogsteen base pair is a minor variation of base-pairing in nucleic acids such as the A•T pair. In this manner, two nucleobases on each strand can be held together by hydrogen bonds in the major groove. A Hoogsteen base pair applies the N7 position of the purine base (as a hydrogen bond acceptor) and C6 amino group (as a donor), which bind the Watson-Crick (N3–N4) face of the pyrimidine base.

Hoogsteen pairs have quite different properties from Watson-Crick base pairs. The angle between the two glycosylic bonds (ca. 80° in the A• T pair) is larger and the C1&prime;–C1&prime; distance (ca. 860 pm or 8.6 Å) is smaller than in the regular geometry. In some cases, called reversed Hoogsteen base pairs, one base is rotated 180° with respect to the other.

This non-Watson-Crick base-pairing allows the third strands to wind around the duplexes, which are assembled in the Watson-Crick pattern, and form triple-stranded helices such as (poly(dA)•2poly(dT)) and (poly(rC)•2poly(rC)). It can be also seen in three-dimensional structures of transfer RNA.

This term is named for Karst Hoogsteen, who, in 1963, first recognized the potential for these unusual pairings (quoted from Lehninger Principles of Biochemistry by David Nelson and Michael Cox, 4th edition, published in 2005 by Freeman).