When bound on the DNA, adenine pairs up not with its fellow purine guanosine, nor with simply either of the two pyrimidines, but specifically with thymine. Similarly, guanosine only pairs with cytosine.

The ability for these four to identify their appropriate partners must come down to some substructural difference, as they are each quite similar in many ways. What's more, is that somehow these molecules must carry identifiable information - otherwise the DNA would be unable to carry or distribute meaningful data.

The purines are divided by these strucures...

common form    adenine   guanosine

Something in these two structures must be crucial to their identification by their corresponding pyrimidines. We'll compare these structures more closely, eliminating everything but the frame...

Adenine   Guanosine

Then, finally, removing everything but the bonds...

A           G

The two substructural bonds (in blue) differ only in terms of the direction of the double bond: One stays in the loop, while the other is externalized.

When we compare the pyrimidines, we get strikingly similar results. 

Here, again, are the two whole structures...

Following the same basic rules we applied to the purines, we get...

T                 C

Going the final step, and rotating the component slightly counterclockwise, we get...

T            C

But how would adenine distinguish thymine from guanosine on these terms of comparison? For the next step, we'll look at all four nucleotide bits together:

Notice the double bonds at the bottom? The purines face inward, while the pyrimidines face outward. This means that adenine could differentiate between thymine and guanosine from the lower bonds, and thymine and cytosine from the upper bonds. The externalized double bonds  are always terminated in oxygen, as you can see here...

Before we continue with this point, we need to do a little math...

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