Double Helix Stability and Base Composition:

In general, helical stability is linearly related to fractional G+C base pair content in DNA. As G+C increases so does stability (Figure 21). An empirical formula for calculating the melting temperature of a particular helix is given as T_m (°C) = 69.3 + 41 * fG/C. This expression quantifies the observed result that there is a linear relation between Tm and G+C content. This observation argues that the energetic contributions of the bases in the helix to its stability are independent and therefore additive--->this implies that stabilization energies are sequence independent. That is the base pairs are all contributing equally and independently a constant amount of stacking energy, independent of the neighbors.

Figure 4.14: Double helix stability depends on base composition.

Helical Stability and Salt

It has been long observed that multiple stranded polynucleotide helices are stabilized by increasing monovalent cation concentration (Figure 4.15). In fact the Tm of a given DNA is linearly dependent on the log of the monovalent cation concentration. We will not spend a lot of time on the polyelectrolyte behavior of nucleic acids, but instead we will simplify the treatments and take an empirical and thermodynamic approach.

Figure 4.15: Double helix stability depends on salt concentration.

The DNA phosphate backbone is negatively charged. In salt solutions, cations are associated with it. When DNA is denatured fewer total cations are associated with the separated strands than with the nucleic acid helix in its native state. This is because the charge density on double stranded DNA is higher than single strand nucleic acids. This creates a larger electrostatic potential, which more effectively attracts counter ions.

Thus, in the denaturation reaction, the mass action equation can be written.
DNA (Helix). Mx <----> DNA(Coil) My + M(x-y)
x= no. of ions bound/base pair in a helix
y= no. of ions bound/base in a coil
x-y = net gain in free cations due to denaturation

Therefore, the denaturation reaction equilibrium can be shifted by adjusting the cation concentration. We have already discussed that effect of temperature on helix → coil transition. The two effects can be balanced at particular conditions. That is if the salt is raised, increases helix potential, can increase temperature to denature.
We have only discussed here the effect of monovalent cations on structure. The effects of divalent cations are much more complex due to their multiple interactions with the DNA phosphate backbone-each M²⁺ can potentially bind one or two DNA phosphates and the binding is likely to be cooperative. Hence, the Tm dependence on divalent cation concentration is decidedly non-linear.