Forces that cause nucleotide bases to stack

The hydrogen bond: everything for everyone

Hydrogen bonds are important in many areas of our life, not just for nucleic acid structure. It is the hydrogen bond that gives water most of its unique properties, and life depends on these properties of water. When we want to know if a planet, moon or asteroid has living organisms, we ask "is there water?".

The structure of water is fluid (no pun intended) in that the molecules are constantly moving while making and breaking hydrogen bonding patterns with neighboring molecules. However, the fundamental bond is seen in this figure, where an electron pair of oxygen is partially shared with a hydrogen atom of another water. The sharing is favored by the partial positive charge on the H atom and the partial negative charge on the O atom. The energy of a hydrogen bond is about 1/10 th as large as the energy of a typical covalent bond.

The hydrogen bonds that characterize the A:T and G:C base pairs are similar, but one or both of the negative atoms is a nitrogen, and the bond separation is about 2.0 A.

Two water molecules caught in a strong hydrogen bond.

[charges proposed by Jorgensen et al., J Chem Physics, 79: 926; 1983 As reported by Tinoco et al., Physical Chemistry, 3rd ed. Prentice-Hall, 1995 , p461]

Water likes itself, or something it can hydrogen bond with

The relatively strong bonding between water molecules stabilizes liquid water, so it has a high boiling point for its molecular weight and a high heat of vaporization. The bonding also makes unfavorable configurations in which the most water is not next to more water. This results in a high surface tension, which tends to minimize the water-anything surface, unless water can hydrogen bond to, i.e. wet, that surface. Water does not bond to the planar faces of the nucleotide bases, thus the bases will stack when they come into close contact in order to decrease the surface area of the water. Thus, the configuration of the two bases in the lower panel is preferred, since the surface over which water can't bond to itself is less. Nucleotide bases will stack, i.e. aggregate, when the monomers are dissolved in water (they are not very soluble, as you would expect).

The structure of water near a surface is often more structured than in the liquid, and this ice-like structure thus represents a decrease in entropy, which would also favor the stacking seen in the left lower panel. This may even be the dominant factor, but we are in deep enough water now, so it may be time to go to the next effect.

A pi-electron cloud hangs above and below every nucleotide base

The bases have alternating single and double bonds in the crude diagrams that I have used to indicate the electron density between the atoms. The electrons are actually shared in such a pattern, so that the density between all the atoms is close to 1.5 bonds, and the p orbitals overlap to form a system called a pi orbital. The simple benzene molecule, where all six atoms are equivalent, is pictured at the right. The electron density is uniformly distributed around the ring, and one component of the pi-electron system is the sum of the electron lobes seen here. The sum of all pi-orbitals is symmetric above and below the ring. Rings that stack share pi-electrons, resulting in a favorable configuration.

Stacks of planer systems with multiple conjugated rings are favored even more, thus the purines, particularly guanine, have high stacking energies.

Charges, charges everywhere but not a net charge in sight

Just like the water molecule, most of the bonds in the heterocyclic bases have a significant polar character due to the partial electrostatic charges on the atoms. When the bases are stacked, the charges contribute to the stacking energy. I haven't drawn in a base stacked on this one, but you can imagine that the energy will be highly dependent on the relative position of the two, and that the charges could also destabilize stacking in some orientations.

In addition to the obvious energy terms from point charges, the electrostatic field of one base induce attractive, asymmetrical electronic distributions in the electron distribution of the other base.

Finally, even in the absence of permanent charges, spontaneous fluctuations in charge occur in each base and induce dipoles in the other. This gives rise to the attractive van der Waals force, or London dispersion, with an energy that falls off as R-6.

Enough, enough, bases stack; let's move on with the story...

The charges on the above guanine were those assigned in order to produce the experimentally observed base stacking energy for computer simulations of nucleic acid behavior [Weiner et al., J Computational Chem, 7:230-252; 1986]

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