RNA is Less Stable Than DNA Because of One Lousy Oxygen Atom

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We have two great vaccines so far. One has to be kept in a regular freezer; the other in a mega freezer. This is because they contain RNA, which is unstable, not the more-stable DNA. What sense does this make? For the answer, you'll need to navigate The Dreaded Chemistry Lesson From Hell! Enjoy. Hint: It's one lousy oxygen atom.

My most excellent colleague Dr. Alex Berezow recently wrote about the instability of the Pfizer vaccine. In the interest of boring all of you to death, I figured it might be a good (?) idea to look at this instability at the molecular level. Hence, it should come as no surprise that it's time for TDCLFH!TM

What is going on is actually a rather simple, well-known chemical reaction called ester hydrolysis – the breaking of an ester bond by water, producing a carboxylic acid and an alcohol (Figure 1)

Figure 1. Hydrolysis of an ester forms a carboxylic acid and an alcohol. The red boxes show where the water has been added. The blue hatch line shows the bond that is broken in the reaction. 

Phosphate esters, the backbone of DNA and RNA, can also be hydrolyzed. The process (Figure 2) is conceptually identical to that of esters. 

Figure 2. Hydrolysis of a phosphate ester. The red squares show where the water has been added. The blue hatch line shows the bond that is broken in the reaction. 

What does any of this have to do with the instability of the Pfizer vaccine?

I apologize in advance, but we're going from organic 101 to organic 401. Please bear with me. I'll be as gentle as possible.

Anchimeric assistance (Neighboring group participation): Why RNA is unstable.

For reasons best left unstated, when a hydroxyl group (1) is either five or six atoms away from either the C=O (carbonyl, carbon-oxygen double bond) or P=O (phosphoryl, phosphorous-oxygen double bond) group where a reaction is taking place, that reaction is accelerated. This is called anchimeric assistance (or neighboring group participation) and its effect can be significant (Figure 3).

Figure 3. Comparative hydrolysis rates of two esters.

If you haven't hung yourself by now, bear with me and I'll show you what all this gibberish has to do with RNA. 

Figure 4 demonstrates the concept of neighboring group participation, but why the difference? It makes no sense. Except it does. This is one reason people hate chemistry.

Figure 4. Anchimeric assistanceThings should be starting to get ugly right about now. Good luck. 

Both of these figures are different representations of the same molecule. They are drawn in different configurations, but it's still the same molecule.  

Now you can see why I've drawn the stupid molecule this way. When the hydroxyl (OH) group is 5 atoms from the carbonyl group it is within perfect bonding distance to react with the carbonyl (C=O) group (Figure 5).

Figure 5. The reaction of 4-hydroxybutyric acid methyl ester to gamma-butyrolactone is promoted by the hydroxyl group. First, the 4-hydroxybutyric acid methyl ester reacts with itself to form gamma-butyrolactone. This reacts with water (green hatch line) to complete the hydrolysis reaction. This is an example of neighboring group participation. (2)

What does this have to do with unstable RNA vaccines?

A lot. Here's why. It's anachiometric assistance again, this time with phosphorous instead of carbon (Figure 6).

Figure 6. (Left) As in Figure 5, RNA has a hydroxyl group 5 atoms from phosphorous putting it at just the right bonding distance of phosphorous (blue arrow). This promotes the breaking of the phosphate bond (red hatch line) that holds RNA together, (Middle) A cyclic intermediate (which is unstable and reacts with water, completing the hydrolysis) and an RNA fragment (green box) are formed. The RNA is destroyed. (Right) DNA has a hydrogen atom (red) circle in the same location of the hydroxyl group in RNA. Hydrogen does not promote this hydrolysis. This is why RNA (and the mRNA vaccines) are unstable and must be kept cold. 

So, it really just comes down to this:

DNA differs from RNA by one oxygen atom (3). So, the mRNA vaccine is unstable. Ain't chemistry grand?


(1) Nitrogen and sulfur also do this.

(2) This is a pared-down explanation of this reaction. If I added more details you would go into a coma.

(3) There are other reasons that DNA is more stable. They are way beyond the scope of this article.