What are quantum nucleotides?

“Quantum nucleotides” is just a word I made up when I was in high school. In freshman biology, I first learned about nucleotides, and I decided to slap “quantum” in front of it because I thought the combination was funny. I would use the term in conversation as a joke, such as when referring to something that irritated me (“That test was a real quantum nucleotide!”) but eventually, I got asked the question: what is a quantum nucleotide?

I didn’t have an answer because there was no answer - it was nothing, just some nonsense I made up. But over time, I wondered what it was too: I asked Siri one day what it was, and it gave an answer about the quantum relations to nucleotides. I thought about it a bit - a nucleotide was just a name for a specific set of molecules which encoded genetic information in RNA or DNA. All molecules were fundamentally quantum - that is, they can be described by quantum mechanics, as can any system, although for an atomic system like that it’s a lot more applicable. So, that made me think - what can a quantum nucleotide be? What could it describe? Well, it’s important first to dive into what is quantum about nucleotides.

A nucleotide is a molecule consisting of hydrogen, oxygen, nitrogen, and carbon. These are the basic building blocks of organic compounds, as they can form many interesting bonds unlike any other atoms, especially carbon, although in proteins nitrogen plays a large role. The basic building block of a nucleotide ring is nitrogen. Nitrogen forms a ring-like structure because they are aromatic, which means they have a delocalized pi-electron system. This just means that the electrons in the system aren’t bound to one atom, but to multiple atoms, within a bond - a bond of course being the electrostatic attraction between the electrons and nuclei of two atoms. A pi-electron refers to the electron in the pi bond. The pi bond is a type of covalent bond (a covalent bond happens when two atoms share one electron) where the p-orbitals of the two atoms, in this case two nitrogen atoms, overlap parallel to each other. A p-orbital is a type of atomic orbital, with angular momentum quantum number l=1, which describes a region in which the electron (or set of electrons at that energy level) are most likely to be located - it has a kind of stretched-out balloon shape rather than the s-orbital’s round sphere shape.

So essentially, these nucleotides form rings because nitrogen (atomic number 7) has three unbonded electrons, which can form a lot of bonds with other atoms, and when it makes it with itself it forms a super stable configuration in the form of a ring. This ring formation benefits from the delocalization of the electrons, which reduces the energy of the system, contributing to its stability. This is caused by quantum effects - the electron is described by a wavefunction, which, as it sounds, is a wave. A wave can experience constructive effects - when peaks or troughs overlap, they cause each other to be bigger - or destructive effects - when the peaks or troughs overlap, they cause each other to cancel out. Delocalization allows the electrons to experience constructive interference, increasing their probability of being in the pi-bond region, and thus increasing the stability of the system. In general, systems heavily prefer low-energy states, which should make sense, especially if you try to put two identical poles of a magnet together before and see how they repel versus when you put two opposite poles and they attract.

Nucleotides nitrogen rings come in two forms: purines, or double ring configurations, and pyrimidines, or single ring configurations. Purines include adenine and guanine, pyrimidines include cytosine, thymine, and uracil. The reason why there are single and double rings is because of the structure of DNA - a single ring must pair with a double ring to keep the DNA structure balanced. If you had two purines paired together, you would get a bulge in the DNA; if you have two pyrimidines, you would get an inward dip. If you’re wondering why nucleotides and DNA follow such exact geometries, the answer is the same as for most things: natural systems like to minimize energy, and that’s why complex molecules will have planar, symmetrical geometries. After that, nucleotides have a sugar backbone, either a deoxyribose (that means that it’s missing an oxygen atom at the 2’ carbon in the five-carbon ring) or ribose (just a five-carbon ring with an oxygen at the 2’ carbon) molecule. The phosphate group links together different chunks of DNA by the sugars, allowing for polymerization so that the nucleotide can link with other nucleotides. The structure of nucleotides gets a lot more complicated, but the idea is that there’s a lot of quantum stuff going on in them - so really, it’s not wrong to call them quantum nucleotides in the first place, although it probably sounds as strange as calling a baseball a “classical baseball”!

So, nucleotides are quantum - what then? There seems to be easy, well-observed answers to the quantum phenomena in these systems. Well, this isn’t totally true, and it goes into limitations of our understanding of quantum mechanics. First, as I said before, the ring structure of the nucleotide means that electrons are delocalized. This means that, if you want to capture this behavior, you have to consider the multi-electron wavefunctions, which are hard to describe, and use density matrix renormalization groups to accurately calculate the energies. The hydrogen bonds between the base pairs are especially quantum, involving proton tunneling and zero point motion. It’s thought that some of the mutations in DNA are caused from spontaneous tautomeric shifts (when a base changes from one isomer to another) through proton tunneling in the nitrogen atoms. There are many interesting quantum effects going on in nucleotides, which have broader impacts on the overall biology of an organism.

Exploring nucleotides from a quantum perspective is an exciting avenue - something that I think would be cool to turn from a silly phrase to an actual, well-developed idea. We often take for granted that DNA is a stable, static structure, but when you peel back the layers, you find a system in constant flux at the quantum level. Electrons delocalize across aromatic rings; protons tunnel between atoms; vibrational zero-point energies shift conformations—and all of this can subtly, or dramatically, influence genetic expression and mutation. By studying these processes, we not only gain insight into the fundamental mechanisms of life, but also lay the groundwork for technologies that could harness these quantum-biological effects: from ultra-sensitive biosensors to quantum-inspired models of replication and repair. In the end, maybe quantum nucleotides wasn’t such a silly little phrase after all.