On the standard B-DNA helix, the phosphate backbone surrounds the base pairs that is at the center of a helix. As a result, two types of grooves can be observed (Fig. 1). The major groove is wider and the minor groove is narrower.
Fig. 1 The ball and stick (left panel) and space filling (right panel) models of a DNA dodecamer. (The grooves were labeled incorrectly, need modification)
The glycosidic bonds of a DNA base pair are the boundaries to define major and minor grooves. As shown in Fig. 2, the major groove (upper part) cover a larger angle than that of the minor groove (lower part). In fact, this description is the operational definition of grooves.
Fig. 2 The location of grooves on a base pair.
因為主溝槽的夾角(about 200度)較大，所以在螺旋轉一圈時所佔的比例也較大。由鹼基對的側面觀察時，看到大於180度的這一側機會較大，而形成比較寬的主溝槽。就B-DNA言,不論由小於180度（副溝槽）或是大於180度（主溝槽）的一側去接近鹼基，其深度都差不多（約15A），而這兩個溝槽的寬度則大約正比於所夾的角度，因為螺旋升高一圈（34A）要轉360度，其中約有13A（34x(160/360)）是看到次溝槽，而有21A（34-13）是看到主溝槽。當然在精確測量實應扣除磷酸酯與五碳醣骨架的寬度，並校正角度所造成的偏差，因此主、次溝槽的寬度分別約為12A與7A。
When the above operational definition is used to examine other types of helix, the major groove may not be wider. For example, in the A-form helix, the major groove is narrower and deeper. Wherea the minor groove is wider and shallower. The main reason is because this definition is based on the initial observation on B-form helix.