Geometry of the double helix

Remember that the two strands are anti-parallel in nature, with the 3′ end of one strand facing the 5′ end of the other strand. The sugar and phosphate of the nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside, like the rungs of a ladder. This is seen in Figure 13a, where the light blue ribbons of the backbone coil around the outside of the helix. One important feature to note is that adenine and thymine form two hydrogen bonds, while cytosine and guanine form three hydrogen bonds, as shown in Figure 13b. Each base pair is a flat structure, roughly trapezoidal in shape. The base pairs form the center of the helix, much like the steps of a spiral staircase, with the sugar-phosphate backbone forming the vertical railing around the outside.

Because each base pair is flat but shaped more like a trapezoid than a rectangle, the base pairs have different dimensions on each side relative to the phosphate groups. The twisting of the two strands around each other thus results in the formation of uniformly spaced major and minor grooves (Figure 13c). On the right face of the helix shown in Figure 13c, the minor groove is labeled. You can see that the red and yellow phosphate groups of the two strands are relatively close together, while on the left side, they are spaced farther apart (labeled as the major groove). This is also seen in Figure 13a, where the cartoon drawing shows the strands alternatingly farther apart and closer together.

The most common form of DNA found in a cell is called B-DNA. In B DNA, Each base pair is separated from the next base pair by a distance of 0.34 nm, and each turn of the helix measures 3.4 nm. Therefore, 10 base pairs are present per turn of the helix. The diameter of the DNA double-helix is 2 nm, and it is uniform throughout due to the consistent pairing of a larger purine with a smaller pyrimidine. These dimensions are also labeled in Figure 13.