A different way to explain the structure of DNA

Here you will get into a visual trip to the structure of the molecule of life. We leave atomic details apart, and focus on the shape of the building blocks of DNA, deoxinucleotides, and how they bind to make up the famous double helix.

By Alfonso Prado-Cabrero, PhD

Double strand of DNA (dsDNA)

DNA is made up of deoxynucleotides. Getting familiar with these building blocks and how they shape DNA opens the door to understanding genetics. In contrast to the classic approach, I believe that less chemical details plus plenty of animations helps to start getting familiar with the molecule of life. Therefore, here we do not get into the detail of atomic composition of DNA. Instead, we focus on 3D structure with animations (maybe they take a while to load). In this way, I hope you become familiar with DNA from all angles.

Deoxynucleotide structure overview

We can define DNA structurally as an spiral staircase, where each deoxynucleotides would be part of both one rail and half rung. In Fig. 1 we show the shape of dAMP, one of the four deoxynucleotides that make up DNA. The 5-deoxyribose (in green) and the phosphate group (in orange) would form part of the rail; the nitrogenous base (in blue), would make up half a rung.

Figure 1. dAMP (deoxyAdenosine MonoPhosphate) represented as ball (atoms) and sticks (bonds between atoms).

This is how deoxynucleotides bind together

Now let’s put together three dAMPs, which bonded form a single DNA strand (Fig. 2). The same coloring pattern of Fig. 1 is used, to make it clear which part of the deoxynucleotides are forming the rungs and which part is forming the rail. But with this, it looks like that we are building only half side of the spiral staircase…

Figure 2. Three dAMPs in a row.

To complete the staircase, we add the complementary chain and we end up with a double strand of DNA (Figure 3). But the newly added strand has the nitrogenous bases colored in light blue. Yes, they are different from adenine. These are thymines.

Now, for note, did you notice that the last phosphate is pointing up in one strand and down in the other? This means that both strands run in opposite directions. DNA double helix is antiparalell. Why antiparalell? Researchers have recently suggested that this seems to help with DNA replication (Subramanian et al., 2020).

Figure 3. Double strand of DNA (dsDNA) composed of 3x dAMPs and 3x dTMPs.

Now let’s step back and focus on the pair of deoxynucleotides at the top of the DNA helix from the previous Figure.

Figure 4. dAMP and dTMP, side view.

Four deoxynucleotides make up DNA

Let’s take a top view of the pair of nucleotides of Fig. 4. Now you can see the nitrogenous bases clearly. Adenine (blue, left) and thymine (light blue, right). Both with their striking planar shape (Fig. 5).

Figure 5. dAMP and dTMP, top view.

And yes, you noticed them. What are those dashed lines? These lines symbolize the bonds that keep the two deoxynucleotides attracting to each other. These bonds, all along the DNA molecule, keep both strands of the double helix together. They are called hydrogen bonds.

Now, below we introduce the other pair of deoxynucleotides that forms part of DNA: dGMP (with guanine as nitrogenous base, in red) and dCTP (with cytosine as nitrogenous base, in pink). Did you notice that this pair of nitrogenous bases establish three double bonds between them, instead of two, like in A=T? This difference is essential: Adenine can only pair with Thymine, and Guanine only pairs with Cytosine.

Figure 6. dGMP and dCMP, top view

Therefore, we deduce that the sequence of deoxynucleotides in one strand unfailingly determines the sequence of deoxynucleotides in the other. Hence, both strands are said to be complementary. Below you can see, for clarity, one of the strands of DNA with the nitrogenous bases colored as above, so you can see the sequence of deoxynucleotides.

Figure 7. Single strand of DNA (ssDNA)

And now we add the other strand, and we get the double strand of DNA, and the complete staircase: two rails and rungs made up of two pieces each one.

Figure 8. Double strand of DNA (dsDNA)

In a future post I will dive into the atom structure of deoxynucleotides, and how their specific bonding patterns give nitrogenous bases their special shape and their capacity to establish hydrogen bonds. 

Alfonso Prado-Cabrero is a research fellow at Nutrition Research Centre Ireland, Waterford Institute of Technology. He is specialised in molecular biology, biotechnology, genetics, carotenoids and fatty acids

The molecules appearing in this post have been built using Avogadro: Hanwell, M.D., Curtis, D.E., Lonie, D.C. et al. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminform 4, 17 (2012). doi: 10.1186/1758-2946-4-17

These molecules have been rendered using UCFS ChimeraX: Pettersen, EF, Goddard, TD, Huang, CC, et al. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Science. 2021; 30: 7082. doi: 10.1002/pro.3943

The videos created with UCFS ChimeraX have been converted to animated gifs using Ezgif