abasic

Abasic is an adjective used in chemistry and biology to describe a molecule that lacks a base, most commonly referring to an abasic site in nucleic acids. An abasic site, also called an AP site, is a position in DNA or RNA where a purine or pyrimidine base is missing while the sugar-phosphate backbone remains intact. The term abasic is often used as shorthand for AP sites that arise in DNA damage and repair contexts, though it can describe other base-free contexts as well.

Formation: Abasic sites form spontaneously through depurination (loss of purine bases) under physiological conditions, and pyrimidines can be removed by specific glycosylases during base excision repair. They can also be generated by chemical mutagens, oxidative stress, or ionizing radiation.

Biological consequences: The absence of a base disrupts base pairing and distorts the DNA helix, impeding replication and transcription. If left unrepaired, AP sites increase mutational risk and may contribute to genome instability. They are major intermediates in the base-excision repair pathway.

Repair: Repair proceeds via base-excision repair. AP endonucleases nick the backbone at the AP site; a DNA polymerase fills the gap and a ligase seals it. In humans, APE1 is a key AP endonuclease; polymerase β and other factors complete restoration. Bypass of AP sites by specialized polymerases can occur but may be error-prone.

Detection and study: AP sites can be detected using aldehyde-reactive probes that label the exposed sugar moiety, among other biochemical assays. The study of abasic sites informs fields such as aging, cancer biology, and the understanding of DNA repair mechanisms.