Non-covalent interactions
A hydrogen bond (H-bond), is a specific type of interaction that involves dipole-dipole attraction between a partially positive hydrogen atom and a highly electronegative, partially negative oxygen, nitrogen, sulfur, or fluorine atom (not covalently bound to said hydrogen atom). It is not a covalent bond, but instead is classified as a strong non-covalent interaction. It is responsible for why water is a liquid at room temperature and not a gas (given water's low molecular weight). Most commonly, the strength of hydrogen bonds lies between 0 - 4 kcal/mol, but can sometimes be as strong as 40 kcal/mol In solvents such as chloroform or carbontetrachloride one observes e.g. for the interaction between amides additive values of about 5 kJ/mol. According to L. Pauling the strength of a hydrogen bond is essentially determined by the electrostatic charges. Measurements of thousands complexes in chloroform or carbontetrachloride have led to additive free energy increments for all kind of donor-acceptor combinations.
GC-content
Qualitativelty, G (guanine) and C (cytosine) undergo a specific hydrogen bonding, whereas A (adenine) bonds specifically with T (thymine, in DNA) or U (uracil, in RNA). Quantitativelty, the GC pair is bound by three hydrogen bonds, while AT and AU pairs are bound by two hydrogen bonds. To emphasize this difference in the number of hydrogen bonds, the base pairings can be represented as respectively G≡C versus A=T and A=U. DNA with low GC-content is less stable than DNA with high GC-content; however, the hydrogen bonds themselves do not have a particularly significant impact on stabilization, the stabilization is due mainly to interactions of base stacking.
In spite of the higher thermostability conferred to the genetic material, it has been observed that at least some bacteria species with DNA of high GC-content undergo autolysis more readily, thereby reducing the longevity of the cell "per se". Due to the thermostability given to the genetic materials in high GC organisms, it was commonly believed that the GC content played a necessary role in adaptation temperatures, a hypothesis that was refuted in 2001.
However, it has been shown that there is a strong correlation between the prokaryotic optimal growth at higher temperatures and the GC content of structured RNAs (such as ribosomal RNA, transfer RNA, and many other non-coding RNAs). The AU base pairs are less stable than the GC base pairs previously attributed to GC bonds containing 3 hydrogen bonds and AU having only 2 hydrogen bonds, making high-GC-content RNA structures more resistant to the effects of high temperatures.
More recently, it has been proved that the most stabilizing factor of thermal stability of double stranded nucleic acids is actually due to the base stackings of adjacent bases, rather than the number of hydrogen bonds between the bases.There is more favorable stacking energy for G:C pairs because of the relative positions of exocyclic groups than in the A:U pairs. Additionally, there is a correlation between the order in which the bases stack and thermal stability.