Phosphodiester bond: mechanism and explanation
Phosphoric acid is esterified with two alcohols: a phosphodiester forms. In DNA and RNA exactly this bond links the 3′-OH of one nucleotide to the 5′-OH of the next.
Example
As a model the two sugars are replaced by methyl groups (dimethyl phosphate). In the strand this creates the sugar–phosphate–sugar backbone, with the bases attached at the side.
Mechanism step by step
- 1
In the cell a nucleoside triphosphate is used as the activated building block.
- 2
The 3′-OH of the growing strand attacks the α-phosphorus (polymerase, Mg²⁺).
- 3
Diphosphate leaves; the new 3′,5′-phosphodiester bond extends the strand by one nucleotide.
To read
This topic is part of the syllabus but not in the training: polymers consist of repeating units and biomolecules react through enzymes in the cell. There is no clear-cut task with exactly one product for it.
Go to the trainer with 157 reactions to practiseBackground
Where the bond occurs
Phosphodiester bonds form the backbone of DNA and RNA: sugar and phosphate alternate, with the bases hanging off the side. Phospholipids in cell membranes and messengers such as cAMP also contain a phosphodiester group.
How the cell makes it
Polymerases add a nucleoside triphosphate to the free 3′-OH of the growing chain. The 3′-OH attacks the inner (α) phosphate and pyrophosphate is released. Splitting that pyrophosphate into two phosphates makes the reaction practically irreversible. That is why nucleic acids always grow in the 5′→3′ direction.
Why RNA breaks down more easily than DNA
In RNA the ribose has a 2′-OH group. It can attack the neighbouring phosphodiester bond from inside (especially under basic conditions), a cyclic 2′,3′-phosphate forms and the chain breaks. DNA lacks this OH group, so it is chemically far more stable and suits long-term storage.
Frequently asked questions
Why is RNA less stable than DNA?
The 2′-OH of ribose can attack the neighbouring phosphate under basic conditions and cleave the strand. DNA (2′-deoxyribose) lacks this group.
In which direction is a strand read?
From 5′ to 3′: new nucleotides are always attached to the 3′-OH end.
What is a phosphodiester bond?
A phosphate group esterified with two hydroxy groups. In DNA and RNA it joins the 3′-OH of one nucleotide to the 5′-OH of the next.
Why is the DNA backbone negatively charged?
Each phosphodiester keeps one oxygen on phosphorus that is deprotonated at pH 7, so every phosphate carries a negative charge.
Which enzymes cleave phosphodiester bonds?
Nucleases: exonucleases remove nucleotides from the ends, endonucleases (such as restriction enzymes) cut within the strand. Phosphodiesterases also cleave cAMP and cGMP.