Other than hydrogen bonding, what else contributes to the stability of the double helix? Solution Apart from the hydrogen bonds between purines and pyramidines, the base stacking interactions with the nucleotides play a very important role in stability of the DNA double helix. Two to three nucleotide rings stack on each other parallelly lije stack of coins to prevent contact with water. stacking also involves a combination of van der Waals and dipole-dipole interactions between the bases..