We’ve seen that the logic of protein structure entails the covalent linkage of a pattern of noncovalent interactions. This is how we encode a three-dimensional reality in one-dimensional terms. And all of this was made possible by the fact that amino acids are linked together in a way where their side chains were not involved in the linkage and thus served more like appendages.

But we have also seen this very logic is at play when it comes to the formation of a chain of nucleotides. As with the side chains of amino acids, the nitrogenous bases can interact with each other through noncovalent forces causing the nucleotide chain to fold into a three-dimensional structure. This is what happens with a lot of RNA and explains its ability to function as a catalyst. But let’s turn to DNA.

With DNA, two nucleotide chains, running in opposite directions, form the well-known double-helix. The thymines on one strand hydrogen bond with the adenines on the other strand, while the guanines hydrogen bond with the cytosines. But it’s more than this. If we look down the end of the DNA double helix, we’d see something similar to the picture shown below.

You can notice one set of base pairs highlighted in white. But as the two strands wind around each other, note how the base pairs stack on each other (the inner circular structure) while the sugar and phosphate groups surround them. This is because the bases are hydrophobic and are thus shielded from the water by the surface sugar/phosphates. And what this means is that it is hydrophobic forces that drive the two strands together, where the hydrogen bonds simply add an additional layer of stabilization coupled to specificity.

The same logic thus applies when forming the double helix of DNA and the folded protein. Both are linear molecules, where a particular sequence is connected together by covalent bonds. Both have appendages that that interact with each other via a pattern of noncovalent forces. Hydrophobic forces collapse a protein into a compact structure and electrostatic forces impart further stability and specificity. Hydrophobic forces drive the double helix together and electrostatic forces impart further stability and specificity. Globular proteins have a hydrophobic core and a hydrophilic surface. The DNA double helix has a hydrophobic core and a hydrophilic surface. And perhaps most remarkable is that Monod’s observation equally applies to both:

The result is that structures defined by noncovalent interactions can attain a certain stability only if they entail multiple interactions. Furthermore, noncovalent interactions acquire a notable amount of energy only when atoms lie a very short distance apart, practically “touching” one another. Consequently two molecules (or areas of molecules) will be able to contract a noncovalent association only if the surfaces of both include complementary sites permitting several atoms of one another to enter into contact with several atoms of the other.

In essence, this is variation on the same logical theme. Same story; different play.

The main differences are twofold: 1.) The pattern of “touching” in the DNA molecule is what codes for the pattern of “touching” in a protein; 2) the sequence of bases on one strand of DNA are complementary to the other strand, meaning the pattern of “touching” in the DNA molecule also “codes” for efficient replication. As I write in The Design Matrix:

The fact that DNA exists as a double helix of two nucleotide chains foreshadows the manner in which the structure of DNA is perfectly suited for replication. To replicate DNA, all you need to do is unwind the two strands and then use each strand as a template for the synthesis of a new, complementary strand. In one molecule, there are two perfect solutions for two design problems—coding the machinery of life and perpetuating the information across time. A more beautiful molecular expression of the form-function relationship would be hard to imagine. Seen from this vantage point, the very structure of DNA is evidence that indicates life was designed to reproduce.

The differences thus complement the similarities and become one.
But what happens when the protein theme meets the DNA theme? What happens when the proteins “touch” the DNA?