Hydrogen-bond donor and acceptor atoms in the major and minor grooves of DNA. (a) Shown here are the functional groups (in red) of all four base pairs as displayed in the major and minor grooves. Hydrogen-bond donor and acceptor atoms that can be used for base-pair recognition by proteins are indicated by light brown and blue squares, respectively. Other hydrogen atoms are indicated by purple squares, and methyl groups by yellow squares. (b) The atoms (color-coded as shown on the right) that can be used for protein recognition for each base pair are grouped as sets of four in each major groove (left) and as sets of three in each minor groove (middle). Notice how the sequence of the atoms in both the major and minor groove differs for the different base pairs, and how the four possible base pairs are chemically distinct in the major groove but not in the minor groove.