What is an AP Site and How Does it Damage DNA?
Learn how the loss of a single base in DNA, an AP site, presents a common challenge to genetic integrity and the biological systems that maintain it.
An organism’s DNA is under constant assault, and one of the most frequent forms of damage is the creation of an AP site. The term “AP site” stands for apurinic/apyrimidinic, describing a location in the DNA’s double helix where a purine (adenine or guanine) or a pyrimidine (cytosine or thymine) base has been lost. Despite the absence of this “letter” in the genetic code, the structural sugar-phosphate backbone of the DNA remains unbroken.
These lesions are remarkably common, with estimates suggesting that a single human cell can generate tens of thousands of them every day. This creates a point of weakness where genetic information becomes unreadable.
How an AP Site Forms in DNA
The formation of an AP site in DNA occurs through two main pathways. The most common origin is spontaneous hydrolysis, a chemical reaction driven by the thermal energy and aqueous environment within a cell. This process involves the breaking of the N-glycosidic bond, which tethers the base to the deoxyribose sugar of the DNA backbone. Purines (adenine and guanine) are significantly more susceptible to this cleavage than pyrimidines, a phenomenon known as depurination.
AP sites are also intentionally created by the cell’s machinery as an intermediate step during base excision repair (BER). Specialized enzymes called DNA glycosylases patrol the genome for damaged bases and actively sever the N-glycosidic bond to remove them. This action generates a temporary AP site that signals for the next stage of the repair pathway.
Why AP Sites Are a Threat to DNA Integrity
An AP site presents a problem for a cell because it disrupts the functions of DNA. The site itself is a non-coding lesion, meaning it contains no genetic information for the cellular machinery that reads DNA. When a DNA polymerase enzyme encounters an AP site during replication, it cannot determine which nucleotide to add to the new strand. This lack of information can cause the polymerase to stall, halting the replication process.
This same issue affects transcription, the process of creating an RNA copy of a gene, as RNA polymerase is also blocked by the AP site. Furthermore, the abasic site is chemically unstable. The sugar at the baseless site is prone to opening its ring structure, which can trigger a reaction that leads to a break in the sugar-phosphate backbone, converting a simple missing base into a more severe single-strand break.
The Cellular Repair Process for AP Sites
To counter the constant formation of AP sites, cells employ a process known as Base Excision Repair (BER). This multi-step pathway acts like a “cut, patch, and seal” operation to restore the DNA’s integrity. The first step involves the recognition of the AP site by an AP endonuclease. In humans, the primary enzyme for this task is APE1, which identifies the baseless sugar and makes an incision in the DNA backbone adjacent to the AP site, creating a nick.
With the site exposed, a specialized DNA polymerase arrives to perform two functions. It first removes the dangling sugar-phosphate remnant of the original damaged nucleotide. Then, using the opposite DNA strand as a template, it inserts the correct, complementary nucleotide into the gap. This ensures the genetic information is accurately restored.
The final step is carried out by an enzyme called DNA ligase. This molecule’s job is to seal the nick in the sugar-phosphate backbone. By forming the final chemical bond, DNA ligase makes the strand whole again and completes the repair process.
Consequences of Unrepaired AP Sites
When the BER pathway fails or is overwhelmed, unrepaired AP sites can have severe consequences. If a cell replicates its DNA with an AP site present, the lesion can lead to mutations. Standard DNA polymerases halt at the site, but cells can use specialized translesion synthesis (TLS) polymerases to bypass the damage. These TLS enzymes are less precise and insert a base opposite the blank site, essentially guessing at the information.
This process is error-prone. TLS polymerases often insert an adenine (A) opposite the AP site, a tendency known as the “A-rule,” which can result in a permanent mutation. These mutations can alter gene function, potentially contributing to diseases like cancer.
The accumulation of unrepaired AP sites can also trigger broader cellular responses, including:
- Cell cycle arrest to allow time for repairs.
- Apoptosis, or controlled cell death, if damage is too extensive.
- Contribution to the long-term aging process.
- Onset of various age-related diseases.