What do the extra lines on nucleotide diagrams mean?

I’m studying for a test and have been looking at a bunch of diagrams of DNA and RNA and most of them have extra lines on the inside of the nitrogenous base geometry. Such as here. At first I assumed they were double bonds but in diagrams drawn using the bond-line structures I’m actually familiar with the double bonds are in very different places, example here. For example on the first diagram there’s a double line on the two carbons that are shared by the adenine rings, on the second there’s no double bond there.

So as the title says I’m curious what the double lines means. Also is there a name for that style of diagram so I can look up more about it? I certainly run into it often enough but I’ve never seen it or it’s syntax explained anywhere and I haven’t had any luck googling it since I’ve no clue what it’s called.

It’s not unique to nucleotides. It is a means of representing bonds in ring structures in organic chemistry. Same as you might see in a drawing of benzene or such in intro to organic chem.


The nature of such ring structures is that it is more like a 1.5 bond between each carbon than a true single/double bond alternation as you go around the ring structure of benzene and similar molecules.

I think they’re just double* bonds. Exactly the same as in the structure in wikipedia for adenine: https://en.wikipedia.org/wiki/Adenine[https://en.wikipedia.org/wiki/Adenine](https://en.wikipedia.org/wiki/Adenine)

  • But with the aromatic rings, the bonds aren’t strictly single or double; all the bonds are partly-single partly-double. So often you can draw the same molecule with double or single bonds in different places, and be just as correct. Have you covered benzene rings and resonance in your chemistry?

As already said, they’re double bonds. If you look at the two representations you can see that all the atoms have the same number of bonds in both configurations.

You can probably also learn something from this Aromaticity - Wikipedia

Double post. Self reported.

They are meant to represent double bonds; note that in your diagram from Purdue the two nitrogens in the 5-ring (imidazole ring? I forget) do not have side bonds associated with them, which is a different structure than is required in adenosine. In general, tautomers are isomers of the same molecule that differ in the position of a hydrogen and a double bond. Some of the tautomers for free adenineare not allowed for adenosine, which requires an external bond to one of the N in the five-ring.

I agree that the Purdue structure for free adenine looks unusual. I wonder if it’s energetically unfavorable compared to the aromatic 6-ring version?

Basically, those would be called a “structural formula.” As opposed to a molecular formula, wherein someone writes C5H5N5 and expects you to know they mean adenine.

Try here for the very basics: How to draw organic molecules

I can’t do subscripts on this forum easily.

Thanks all, it makes sense to me now.

Since the original question has already been answered, I’ve got one of my own: had you taken organic chemistry previously? I’ve met people who were studying biochem without the most basic knowledge of chemistry; it’s like trying to read Moliere in the original with no prior knowledge of French, but some schools apparently don’t realize this.

Nope haven’t studied organic chem yet. Just went back to school and doing some prereqs for what will be a applied chemistry degree.

This was for the biology prereq I didn’t really need to know anything of the specifics of the chemistry of DNA. I was just looking further than the course required out of curiosity. I have taken a few chem courses but they’ve been super surface level and incredibly easy. The first was basically just the sort of chem you’d learn just from watching basic science documentaries. Subatomic structure, why the periodic table is organized how it is, etc. The second was just some chem algebra. Specific heat, equilibrium constants and that sort of thing.

The first organic chem course on my degree program is still a year away if I were taking it full time. So more like two or three years away as I’m going part time.