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An abasic site (also called an AP site, short for apurinic/apyrimidinic site) is a position in DNA where the base has been lost but the sugar-phosphate backbone is still there. It is a common form of damaged DNA, it can stall polymerases or lead to mutations if left unrepaired, and in human cells the enzyme APE1 normally cuts the backbone at the site as part of base excision repair.
This page is for researchers and lab staff who meet the term in papers, repair-enzyme descriptions or AP-site assay documentation and want a precise, sourced map of what an abasic site is and who handles it.
Definition and scope
In an abasic site the nucleobase (purine or pyrimidine) is missing, while the deoxyribose and the phosphodiester backbone remain. The names “apurinic” (a lost purine) and “apyrimidinic” (a lost pyrimidine) describe which base went missing; “AP site” covers both. Per Li and Wilson (2014), AP sites arise when a base is lost from the backbone through spontaneous hydrolysis, acid or heat, or genotoxin-induced base release, and DNA glycosylases create AP sites as repair intermediates when they remove damaged bases.
How abasic sites form
Spontaneous and chemical damage
The base-sugar bond can break without any enzyme: Li and Wilson list spontaneous hydrolysis, acid or heat, and genotoxin-induced base release. This is one reason abasic sites are treated as a constant background form of DNA damage rather than a rare event.
Intermediates of base excision repair
When a DNA glycosylase removes a damaged base, the product is an AP site. The cell therefore makes abasic sites on purpose, as a step on the way to repairing the original lesion, and then has to process them quickly.
How abasic sites are repaired: the enzymes involved
Two sources agree on the core human pathway (Li and Wilson 2014; Reactome pathway R-HSA-73930, “Resolution of Abasic Sites (AP sites)”, which cites Lindahl and Wood 1999). The table below keeps only the steps those sources state.
| Step | Enzyme | What the sources say it does |
|---|---|---|
| 1. Creates the AP site | DNA glycosylase (or spontaneous loss of the base) | Removes a damaged base, leaving an AP site as an intermediate (Li and Wilson 2014). |
| 2. Cuts the backbone | APE1 (APEX1), a class II AP endonuclease | Cleaves the backbone on the 5′ side of the AP site, leaving a 3′-OH and a 5′-deoxyribose phosphate. Reported as the predominant, if not sole, AP endonuclease in mammals (Li and Wilson 2014). Reactome describes it as displacing the glycosylase and performing the cleavage at the 5′ side of the base-free deoxyribose. |
| 3. Removes the sugar fragment | POLB (DNA polymerase beta) | Recruited to the nick and removes the abasic sugar phosphate (5’dRP) (Reactome R-HSA-73930). |
Damaged DNA and repair enzymes: how the pieces relate
“Damaged DNA” is the broad category; an abasic site is one specific kind of lesion in it. “DNA repair enzymes” in this context means the glycosylases, the AP endonuclease APE1 and the polymerase that finish the job in base excision repair. If the AP site is not processed, Li and Wilson note that loss of the base can cause error-prone bypass synthesis or polymerase arrest, with consequences such as mutagenesis, chromosome instability and gene-expression defects.
For other well-characterised lesions and their repair, see CASRAI’s guide on how UV damages DNA and how thymine dimers are repaired. For a method that detects strand breaks in single cells, see the comet assay guide.
Where it matters in the lab
- Reading the literature. Papers on base excision repair describe abasic sites as intermediates; knowing the order glycosylase, APE1, POLB tells you which enzyme a given experiment is probing.
- Polymerase behaviour. Because an abasic site can cause polymerase arrest or error-prone bypass, a damaged template is a recognised reason a polymerase may stop or misincorporate. How a particular polymerase handles it depends on the enzyme; for one commonly used example see DNA polymerase I and the Klenow fragment.
- Nicking enzymes are a different thing. An AP endonuclease cuts at a base-free site; a nicking endonuclease cuts one strand at a recognition sequence. See nicking endonuclease for the second case.
Common misunderstandings
The “10,000 per day” figure is per genome, not per cell
Li and Wilson (2014) quote Lindahl’s estimate of roughly 10,000 depurination/depyrimidination events occurring spontaneously per mammalian genome per day. The unit is the genome; other reviews express rates differently, so quote the figure with its unit and attribution.
An AP site is not a modified base
It is the absence of a base. The backbone is intact, which is why it can be recognised and cut by APE1.
Abasic site, strand break and nick are different lesions
An abasic site is a missing base; a nick or strand break is a cut in the backbone. APE1 converts the former into the latter as a repair step, which is why a nick can appear after APE1 acts on an abasic site.
FAQ
What is an abasic site in DNA?
A location in DNA where the purine or pyrimidine base is missing but the sugar-phosphate backbone is still present; also called an AP (apurinic/apyrimidinic) site.
What repairs an abasic site?
In human base excision repair, APE1 cleaves the backbone 5′ to the AP site and polymerase beta (POLB) removes the remaining 5′-deoxyribose phosphate, per Li and Wilson (2014) and Reactome.
What happens if an abasic site is not repaired?
It can cause polymerase arrest or error-prone bypass synthesis, with mutagenesis, chromosome instability and gene-expression defects as possible outcomes (Li and Wilson 2014).
Is an AP site the same as damaged DNA?
It is one type of DNA damage. Damaged DNA also includes other lesions, for example thymine dimers from UV light.
Sources
- Li M, Wilson DM III. Human apurinic/apyrimidinic endonuclease 1. Antioxid Redox Signal 2014;20(4):678-707. pmc.ncbi.nlm.nih.gov/articles/PMC3901322 (read 2026-11-07).
- Reactome. Resolution of Abasic Sites (AP sites), single-nucleotide replacement, R-HSA-73930. reactome.org/content/detail/R-HSA-73930 (read 2026-11-07).
