Unit content
DNA ligase and sealing of phosphodiester-backbone nicks
A nick is a break in one strand of a DNA sugar-phosphate backbone when the nucleotides on both sides of the break are still present and aligned within a duplex.
The enzyme DNA ligase seals such a break by forming the missing phosphodiester bond between an adjacent $3'$ hydroxyl and $5'$ phosphate.
Schematically:
... DNA — 3′OH 5′P — DNA ...
↑ nick
DNA ligase
↓
... DNA — continuous backbone — DNA ...
Ligase seals; it does not fill sequence gaps
This distinction is important.
If one or more nucleotides are missing, DNA ligase cannot infer and synthesize those nucleotides. A DNA polymerase must first fill the gap using a template. Ligase can then seal the final nick left between adjacent DNA segments.
Thus a common repair pattern is
remove damaged DNA
↓
gap remains
↓ DNA polymerase
gap filled, nick remains
↓ DNA ligase
continuous backbone
The same chemistry is reused in different processes
DNA ligase performs the same basic backbone-sealing responsibility in several contexts:
- joining Okazaki fragments during lagging-strand replication;
- completing base- and nucleotide-excision repair after resynthesis;
- sealing DNA ends during several double-strand-break repair pathways;
- laboratory assembly of DNA fragments.
The surrounding proteins and DNA structures differ, but ligase's local chemical job is the same: restore covalent continuity where the correct DNA ends are already positioned next to one another.
Separating gap filling from nick sealing makes DNA-repair mechanisms easier to reason about: polymerase reconstructs missing sequence information; ligase closes the remaining backbone discontinuity.