Subtle Bonding

DNA has 2 strands of sugared phosphate groups. Between the strands are nitrogen bases, which contain the physical correlate to genetic information. It has been thought that hydrogen bonds held the strands together. Instead, DNA bonding, and its helical structure, owe to intricacies in existing in a watery environment.

DNA has a natural affinity for its watery environ (hydrophilic). Yet DNA wants its interior dry, so it compacts itself, with base pairs kept tightly together to keep water out.

“The main stabilizer of the DNA double helix is not the base-pair hydrogen bonds but coin-pile stacking of base pairs, whose hydrophobic cohesion, requiring abundant water, indirectly makes the DNA interior dry so that hydrogen bonds can exert full recognition power,” wrote Bobo Feng, Bengt Nordén, and other organic chemists and geneticists.

To prod a DNA strand apart, and so expose itself, an enzyme (catalytic protein) creates a hydrophobic environment at a specific spot. The DNA opens up, letting other proteins copy or repair the strand.

Bobo Feng said, “Cells want to protect their DNA, and not expose it to hydrophobic environments, which can sometimes contain harmful molecules. But at the same time, the cells’ DNA needs to open up in order to be used. The cell keeps its DNA in a water solution most of the time, but as soon as a cell wants to do something with its DNA, like read, copy or repair it, it exposes the DNA to a hydrophobic environment.”


Bobo Feng et al, “Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects,” PNAS (14 August 2019).

Scientists disprove popular theory of how DNA binds itself,” Sci News (23 September 2019).