Hydrogen bond
Hydrogen bonds can be intermolecular (occurring between separate molecules) or intramolecular (occurring among parts of the same molecule). Depending on the nature of the donor and acceptor atoms which constitute the bond, their geometry, and environment, the energy of a hydrogen bond can vary between 1 and 40 kcal/mol. This makes them somewhat stronger than a van der Waals interaction, and weaker than fully covalent or ionic bonds. This type of bond can occur in inorganic molecules such as water and in organic molecules like DNA and proteins.
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.