In these experiments, the chemical variable that is still there to transmit the affect is the water. The affect has to do with the impact the DNA has on the aqueous hydrogen bonding.
One thing we have to remember is a double helix of DNA also has a double helix of water that is built into the DNA. Where science needs to focus is to look at the shape of the combined water when particular areas of the DNA attract each other. The composite water shape may be a larger stable water structure that offers a lowering of system energy. Even if the DNA is moving randomly, once the water hooks up this offers an energy advantage.
The diagram above is only the water within double helix near the base pairing. There is also water that builds on this and then extends outside the DNA onto the surface past the phosphate. The inner water structure will be different for the two base pairs since it is dependent on the groups that can hydrate within each of the four bases.
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Hydration is greater and more strongly held around the phosphate groups that run along the inner edges of the major grooves. The water molecules are not permanently situated however, due to the rather diffuse electron distribution of the phosphate groups. Hydration is more ordered and more persistent around the bases with their more directional hydrogen-bonding ability and restricted space. Water molecules are held relatively strongly with residence times for the first hydration shell being about 0.5 - 1 ns. Because of the regular structure of DNA, hydrating water is held in a cooperative manner along the double helix in both the major and minor grooves.
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What this tells me is hydration around the phosphate groups is not very ordered around a double helix. But it is more so along the inner edges of the major groves. It is likely when similar zones of DNA attract, the hydration ordering around the phosphate increases and offers an energy advantage. It creates a space restriction with the increase in water order a reflection of the more stable hydration of the major grove.
