Nucleic acids and chromatin
Nucleic acids and chromatin

This free course is available to start right now. Review the full course description and key learning outcomes and create an account and enrol if you want a free statement of participation.

Free course

Nucleic acids and chromatin

Base stacking

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.

Figure 6
Figure 6 Base stacking reduces exposure of the hydrophobic bases to the aqueous environment. (a) Simple ‘strands’ diagram of the DNA duplex with the base pairing shown. (b) Pictogram in which each base pair is shown as a single block spanning the duplex and the sugar-phosphate backbones are represented by solid lines, (c) Pictogram showing how stacking results in the bases interacting and twisting, such that the backbone angle is 30°. This twisting produces the helical structure. (d) The intercalation of ethidium bromide, a hydrophobic molecule, between the bases in a nucleic acid duplex (right) results in a chain that is lengthened. (The intercalated ethidium bromide molecules are represented here as orange bars.)

Table 2 Base stacking energies for various adjacent base pairs.

Dinucleotide pair (5′–3′)–(3′–5′) Stacking energy per stacked pair / kJ mol−1
(GC)–(GC) −61.0
(AC)–(GT) −44.0
(TC)–(GA) −41.0
(CG)–(CG) −41.3
(GG)–(CC) −34.6
(AT)–(AT) −27.5
(TG)–(CA) −27.5
(AG)–(CT) −27.1
(AA)–(TT) −22.5
(TA)–(TA) −16.0

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.

S377_1

Take your learning further

Making the decision to study can be a big step, which is why you'll want a trusted University. The Open University has over 40 years’ experience delivering flexible learning and 170,000 students are studying with us right now. Take a look at all Open University courses.

If you are new to university level study, find out more about the types of qualifications we offer, including our entry level Access courses and Certificates.

Not ready for University study then browse over 900 free courses on OpenLearn and sign up to our newsletter to hear about new free courses as they are released.

Every year, thousands of students decide to study with The Open University. With over 120 qualifications, we’ve got the right course for you.

Request an Open University prospectus