AP site

In <a href="/facts/Biochemistry/fa2pWEBp">biochemistry</a> and <a href="/facts/Molecular_genetics/Q8wsm0FE">molecular genetics</a>, an AP site (apurinic/apyrimidinic site), also known as an abasic site, is a location in <a href="/facts/DNA/nB89Iauz">DNA</a> (also in <a href="/facts/RNA/HxPeNfNj">RNA</a> but much less likely) that has neither a <a href="/facts/Purine/9ogLp0Wc">purine</a> nor a <a href="/facts/Pyrimidine/uFRSB8Cq">pyrimidine</a> base, either spontaneously or due to <a href="/facts/DNA_damage/hsURuYYq">DNA damage</a>. It has been estimated that under physiological conditions 10,000 apurinic sites and 500 apyrimidinic may be generated in a cell daily.
AP sites can be formed by spontaneous <a href="/facts/Depurination/uWqchkUh">depurination</a>, but also occur as intermediates in <a href="/facts/Base_excision_repair/QQIlyTxY">base excision repair</a>. In this process, a <a href="/facts/DNA_glycosylase/2V18G016">DNA glycosylase</a> recognizes a damaged base and cleaves the N-glycosidic bond to release the base, leaving an AP site. A variety of glycosylases that recognize different types of damage exist, including oxidized or methylated bases, or <a href="/facts/Uracil/KUAcYYpQ">uracil</a> in DNA. The AP site can then be cleaved by an <a href="/facts/AP_endonuclease/409t29GD">AP endonuclease</a>, leaving 3'-hydroxyl and deoxyribose-5-phosphate termini (see <a href="/facts/DNA_structure/U7sYh5pn">DNA structure</a>). In alternative fashion, bifunctional glycosylase-lyases can cleave the AP site, leaving a 5' phosphate adjacent to a 3' α,β-unsaturated aldehyde. Both mechanisms form a single-strand break, which is then repaired by either short-patch or long-patch base excision repair.
If left unrepaired, AP sites can lead to <a href="/facts/Mutation/Ee4NnWbY">mutation</a> during <a href="/facts/Semiconservative_replication/rJJAglA3">semiconservative replication</a>. They can cause <a href="/facts/Replication_fork/wrU6RuR3">replication fork</a> stalling and are bypassed by <a href="/facts/DNA_repair/hsURuYYq">translesion synthesis</a>. In <a href="/facts/Escherichia_coli/nR4Gvl56">E. coli</a>, adenine is preferentially inserted across from AP sites, known as the "A rule". The situation is more complex in higher eukaryotes, with different nucleotides showing a preference depending on the organism and experimental conditions.

AP site open-in-new

AP site