Hoogsteen base pair

Hoogsteen pointed out that if the alternative hydrogen-bonding patterns were present in DNA, then the double helix would have to assume a quite different shape.

This recognition was originally thought to primarily involve specific hydrogen-bonding interactions between amino-acid side chains and bases.

The resulting variations alter the presentation of DNA bases to proteins molecules and thus affect the recognition mechanism.

For example, stretches of A and T bases can lead to narrowing the minor groove of DNA (the narrower of the two grooves in the double helix), resulting in enhanced local negative electrostatic potentials which in turn creates binding sites for positively charged arginine amino-acid residues on the protein.

Hoogsteen pairs also allows formation of secondary structures of single stranded DNA and RNA G-rich called G-quadruplexes (G4-DNA and G4-RNA).

This permits assembly of planar quartets which are composed of stacked associations of Hoogsteen bonded guanine molecules.

Chemical structures for Watson–Crick and Hoogsteen A•T and G•C+ base pairs. The Hoogsteen geometry can be achieved by purine rotation around the glycosidic bond (χ) and base-flipping (θ), affecting simultaneously C8 and C1 ′ (yellow). [ 1 ]
Base triads in a DNA triple helix structure.