An abasic site represents one of the most frequent types of damage that occurs to the DNA molecule within a cell. This lesion is often referred to by the more technical name of an apurinic/apyrimidinic, or AP, site. DNA is constantly exposed to chemical stresses, meaning damage is a normal, daily occurrence. It is estimated that thousands of these AP sites can be generated in a single human cell every day. These lesions pose a significant threat because they disrupt the genetic code, requiring specialized cellular machinery to quickly identify and correct them.
Structure and Causes of Abasic Sites
DNA is constructed like a twisted ladder, where the sides are formed by alternating sugar and phosphate groups, known as the sugar-phosphate backbone. The rungs of this ladder are the nitrogenous bases—adenine (A), guanine (G), cytosine (C), and thymine (T)—which pair specifically across the two strands. An abasic site occurs when the chemical bond connecting a nitrogenous base to its deoxyribose sugar is broken, resulting in the loss of the base. This leaves the sugar and phosphate backbone intact, but the genetic information at that specific position is missing.
The formation of abasic sites happens through two primary mechanisms: spontaneous chemical breakdown and enzymatic action. The most common spontaneous event is depurination, the natural hydrolytic loss of a purine base (adenine or guanine) from the DNA under normal physiological conditions. Because the chemical bond connecting purines to the sugar backbone is less stable than the bond connecting pyrimidines, depurination happens far more frequently than depyrimidination.
Abasic sites are also created intentionally by the cell as an intermediate step in a major DNA repair pathway. This process begins when specialized enzymes called DNA glycosylases recognize and remove a damaged or inappropriate base. For example, a glycosylase might remove a chemically altered base (like one caused by oxidation) or remove uracil, which should not be present in DNA. By cleaving the N-glycosidic bond to release the damaged base, the glycosylase leaves behind the baseless sugar, thus generating an AP site.
The resulting abasic site is a chemically reactive structure, existing primarily as a ring-closed furanose, but also in a small proportion as an open-ring aldehyde. This aldehyde form is highly susceptible to a reaction called beta-elimination, which leads to the breakage of the DNA strand. If not quickly repaired, the abasic site can also react with other molecules, forming more complex and difficult-to-repair lesions like DNA-protein crosslinks.
Impact on Genetic Information
The presence of an abasic site poses a significant physical and informational challenge to the cell. Since the site lacks a nitrogenous base, it provides no template information, leading to severe consequences during cell division and gene expression. The primary replicative DNA polymerases, responsible for accurately copying the genome, are strongly blocked when they encounter an abasic site.
When the replication machinery stalls at the site, the cell cycle can be arrested, which may ultimately trigger programmed cell death. If the cell attempts to continue copying the DNA, the blockage can result in the formation of single-stranded or double-stranded breaks in the helix, further compromising genomic integrity. To overcome this physical roadblock, the cell can deploy specialized enzymes known as translesion synthesis (TLS) polymerases.
These TLS polymerases are designed to bypass damaged DNA sites, but they do so at the cost of accuracy. When a TLS polymerase encounters an abasic site, it lacks a template to guide the insertion of the correct nucleotide. In many cases, these error-prone polymerases preferentially insert an adenine nucleotide (A) across from the baseless site, known as the “A-rule.” This incorrect insertion results in a point mutation, where the original base pair is permanently changed in the newly synthesized DNA strand.
The mutagenic potential of abasic sites requires prompt repair to prevent diseases like cancer. The incorporation of an incorrect base or a frameshift mutation due to the baseless site can alter the function of important genes. The cell’s survival depends heavily on the efficiency of the repair systems dedicated to addressing these frequent lesions.
How Cells Fix This Type of DNA Damage
The cell’s main defense against abasic sites is the Base Excision Repair (BER) pathway, which is highly efficient at removing these common, non-helix-distorting lesions. BER is a multi-step process that ensures the damaged section is excised and replaced with the correct DNA sequence. The repair process is initiated either by the presence of a spontaneous abasic site or by the action of a DNA glycosylase that created the site by removing a damaged base.
Once an abasic site exists, an enzyme called AP endonuclease recognizes the missing base and cleaves the DNA backbone immediately next to the lesion. This incision creates a break, or nick, in the sugar-phosphate strand, marking the site for removal. Following this incision, the remaining sugar-phosphate fragment at the site must be removed.
In the most common short-patch BER pathway, a specialized enzyme, often DNA Polymerase beta, acts to remove the sugar fragment and simultaneously fill the gap. This polymerase inserts a single, correct nucleotide into the gap, using the undamaged complementary strand as a template. This single-nucleotide replacement mechanism is designed to be highly accurate, preventing the errors associated with translesion synthesis.
The final step in the repair sequence is performed by DNA ligase, which acts as the molecular glue. This enzyme seals the final nick in the sugar-phosphate backbone, covalently joining the newly inserted nucleotide to the existing DNA strand. This coordinated enzymatic effort allows the Base Excision Repair pathway to quickly and accurately remove the baseless site, restoring the original sequence of the genetic information.