Major and minor grooves
The B-DNA major groove is labelled in Figure1a. The terms
‘major groove’ and ‘minor groove’ are based on the two
grooves of the Watson–Crick B-DNA structure. Although
the dimensions of the major and minor grooves are
different for the three different helix families, from the
point of view of the bases, the major groove is always on the
same side for a given base pair. Note that the sugars
(Figure 3a) are closer to one side of the base pair than the
other. There is less space on the side between the sugars
(lower side of the base pair in Figure 3a). The convention is
that the side closest to the sugars is called the minor groove
side.
For B-DNA helices, proteins binding in the major
groove usually bind to specific sequences, often through
the insertion of an a helix into the major groove. In
addition, the major groove of B-DNA is approximately the
correct width to accommodate a third base pair (usually a
pyrimidine), as happens in certain triplex DNA structures.
Proteins that bind DNA nonspecifically (such as
chromatin proteins) will often bind DNA in the minor
groove, through interactions with a protein b strand. In
addition, water molecules and small ions can bind to, and
stabilize, the minor groove. In A-DNA, the minor groove is
almost the same size as the major groove, while in Z-DNA,
the minor groove is deep and narrow, and the major groove
is almost nonexistent.