Although the base pairing brought about by hydrogen bonding is responsible for the specificity of the base interactions, much of the stability of a duplex nucleic acid is due to interactions that result from base stacking. If you look back at Figure 3a, you will notice that, when seen from a side view, our schematic representation of a polynucleotide has a ‘gap’ between each base. Remember that the surfaces of the bases have few polarised bonds; consequently, base surfaces are hydrophobic. As a result, the most energetically favoured conformation is attained by reducing exposure of the base surfaces to the aqueous environment, which is achieved by the bases moving closer together. In this conformation, the backbone is ‘tilted’ by an angle of 30° from horizontal, as shown in Figure 6a–c. Tilting the backbone in this way brings the planar rings of adjacent base pairs to a position where they lie vertically one above the other, an arrangement that maximises hydrophobic interactions and in addition, maximises van der Waals attractive forces between them. To give you an idea of how strong these interactions are along a stretch of DNA, the free energy values for base stacking for various adjacent bases are shown in Table 2. We will see later how base stacking plays a central role in the structure of the DNA double helix.
Table 2 Base stacking energies for various adjacent base pairs.
|Dinucleotide pair (5′–3′)–(3′–5′)||Stacking energy per stacked pair / kJ mol−1|
The hydrophobicity of the bases in duplex DNA is exploited to allow its easy visualisation with a chemical called ethidium bromide. Ethidium bromide (see structure above) is a hydrophobic molecule that, in an aqueous environment, intercalates between stacked bases of DNA as shown in Figure 6d. This has the effect of partially unstacking the bases and lengthening the helix. To the advantage of molecular biologists, this intercalation alters the fluorescent properties of ethidium bromide, allowing us to visualise its interaction with DNA using UV light at 260 nm.