4.12. The Stability of RNA v. DNA

4.13. PHYSICAL PROPERTIES OF DNA

1. DNA base pairs--called complementary base pairing ---- hydrogen bonds between bases.
2. This arrangement of two nucleotides binding together across the double helix is called a base pair.
3. In a double helix, the two strands are also held together via forces generated by the hydrophobic effect and pi-stacking, which are not influenced by the sequence of the DNA.
4. As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily. The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force or high temperature.
5. In the laboratory, the duplex stability can be measured by finding the temperature required to break the hydrogen bonds, their melting temperature (also called Tm value). When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules. These single-stranded DNA molecules have no single common shape, but some conformations are more stable than others.

Figure 4.11: Melting curve of various duplexes shown.

4.14. Stability of Double Helix: Forces in duplex DNA
Since biological processes are regulated, fundamentally, through specific DNA-protein recognition, and DNA protein recognition is controlled by DNA conformation, the study of duplex DNA structure and stability is highly significant. Various Weak Forces come together to stabilize the DNA structure.

1. Hydrogen bonding  (2-3 kcal/mol per base pair)
2. Stacking interactions (4-15 kcal/mol per base pair)
   1. Hydrophobic interactions
   2. van der Waals interactions
3. Charge-Charge Interactions
4. Solvation

These are cooperative forces; each contributes a little, but adds up because DNA chains can be millions of nucleotides long.

• Hydrogen bonds, linkage between bases, although weak energy-wise, is able to stabilize the helix because of the large number present in DNA molecule. Also important that the purine-pyrimidine base pairs are of similar size.

• Stacking interactions, or also known as Van der Waals interactions between bases are weak, but the large amounts of these interactions help to stabilize the overall structure of the helix.

• Double helix is stabilized by hydrophobic effects by burying the bases in the interior of the helix increases its stability; having the hydrophobic bases clustered in the interior of the helix keeps it away from the surrounding water, whereas the more polar surfaces, hence hydrophilic heads are exposed and interaction with the exterior water
• Stacked base pairs also attract to one another through Van der Waals forces the energy associated with a single van der Waals interaction has small significant to the overall DNA structure however, the net effect summed over the numerous atom pairs, results in substantial stability.
• Stacking also favors the conformations of rigid five-membered rings of the sugars of backbone.