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View of helix showing stacking of planar bases.

Stacking is the hydrophobic interaction between the flat surfaces of adjacent bases. It makes a significant contribution to the stability of a nucleic acid in solution.


Nucleic acid bases are flat and vaguely coin-shaped. The edges can form strong interactions with water and other bases through hydrogen bonding, but the large top and bottom surfaces of the base cannot.

These surfaces interact with water in a manner similar to oil. The same forces that cause droplets of oil to merge in water cause the hydrophobic surfaces of bases to clump together into stacks.

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