7.5. DNA vs. RNA
Of the functions that deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) perform in organisms the most common is information storage.
In very broad terms, DNA is used for long-term multi-generational storage. It is typically kept by the cell in a central, chemically protected area. Any given molecule of DNA will need to be stable long-term (decades), with the ability for the cell to confirm that the sequence (instructions) is still correct. It may be helpful to think of DNA as analogous to a blueprint of the design and construction techniques used to make a specific building, kept in a secure repository and maintained/fact-checked over time.
Conversely, one of the roles RNA fills is as short-term information storage. It is located throughout the cell, with some areas having higher amounts or specific sequences. Any given molecule of RNA only needs to be stable short-term (days to months) because the cell can create more as needed. The cell does not typically confirm that the sequence (instructions) is still correct because there are typically many copies of the same molecule (with the same sequence), so a single copy with an error is not typically problematic. It may be helpful to think of this kind of RNA as analogous to a photocopy of a page from the blueprint that describes the techniques used to make a specific part of the building, produced and distributed to the areas that will need to follow that set of instructions.
The two main chemical differences between the structures of DNA and RNA result from the different requirements of long-term and short-term stability.
As the name implies, deoxyribonucleic acid differs from ribonucleic acid by lacking an alcohol/oxygen, specifically at position 2 of the saccharides incorporated into the polymer (Figure 7.21).
Figure 7.21 – Comparison of Generalized Ribonucleic and Deoxyribonucleic Acid Trimers.
The lack of an alcohol at this position has two general effects.
First, its absence makes forming coiled helix structures more favourable by reducing steric interactions in the polymer backbone during twisting. This allows DNA to form helices more easily. For example, in two otherwise identical coiled structures the ribonucleic acid trimer has unfavourable steric interactions that the deoxyribonucleic acid lacks (Figure 7.22).
Figure 7.22 – Comparison of Coiled Structures of Otherwise Identical Ribonucleic and Deoxyribonucleic Acid Trimers.
Second, its absence makes DNA degrade much more slowly. In RNA this alcohol is responsible for the main non-enzymatic degradation pathway. This occurs through an intramolecular nucleophile-electrophile reaction that breaks the polymer (Scheme 7.7). Although this reaction is not relatively fast over the required lifetime of DNA it would cause issues. By removing the alcohol DNA removes this possibility, which greatly increases the molecule’s stability.
Scheme 7.7 – Simplified Mechanism of Ribonucleic Acid Degradation from an Intramolecular Reaction.
Deoxyribonucleic acid differs from ribonucleic acid in one of the nucleobases used: RNA incorporates uracil, while DNA incorporates thymine. These nucleobases differ by the presence of an extra methyl group on the heterocycle (Figure 7.23).
Figure 7.23 – Comparison of Uracil and Thymine Nucleobases Incorporated into Nucleic Acids.
The addition of a methyl at this position has one general effect. Its presence makes proofreading DNA much simpler. The heterocyclic ring of both uracil and thymine undergo a slow but spontaneous transformation over time (Scheme 7.8). The specific details and mechanism are not relevant. Although this reaction is not relatively fast over the required lifetime of DNA it would cause issues. The reaction converts uracil into cytosine, another common nucleobase. As a result, it is difficult for the cell to identify this as an error. For short-term RNA use this is not a problem, but for long-term DNA use it would be. Conversely, thymine also becomes a new nucleobase but it is not one of the common nucleobases. As a result, it is simple for the cell to identify this as an error and make corrections. By adding the methyl DNA greatly increases the feasibility of keeping the sequence error-free.
Scheme 7.8 – Simplified Reaction of Amination of Uracil and Thymine.
