Depurination
Definition
Hydrolytic cleavage of the N-glycosidic bond between deoxyribose and a purine base (adenine or guanine), generating an abasic (apurinic) site. Abasic sites stall DNA polymerases and, if numerous, cause strand breaks. Depurination is the dominant hydrolytic damage pathway at physiological temperatures.
- Mechanism
- Hydrolysis of N-glycosidic bond
- Bases affected
- Adenine and guanine (purines)
- Product
- Abasic (apurinic) site
- Downstream effect
- Polymerase stalling, strand breaks
Common questions
Why does depurination matter more than depyrimidination in ancient or degraded DNA?+
The N-glycosidic bond of purines is intrinsically more labile than that of pyrimidines under physiological conditions, so depurination proceeds faster and dominates the hydrolytic damage seen in aged or environmentally exposed samples.
How do labs work around abasic sites when amplifying degraded DNA?+
Because abasic sites block polymerase read-through, labs favour short amplicon designs, additives that improve polymerase processivity, and repair enzymes such as those used in ancient DNA protocols to reduce the chance a template is unreadable.
Related terms
- 8-Oxoguanine
- An oxidised form of guanine produced by reactive oxygen species attacking the C8 position of the guanine ring. 8-Oxoguanine mispairs with adenine...
- Abasic Site
- A position in the DNA backbone where the nitrogenous base has been lost, leaving only the deoxyribose-phosphate scaffold. Also called an AP...
- Amplicon
- The double-stranded DNA fragment produced between two PCR primers. In forensic STR typing, amplicon size determines whether a locus can be recovered...
- Interlocus Drop-Out
- Failure of larger-amplicon loci to amplify in a degraded-DNA sample while shorter loci succeed. Results in a partial profile that includes only...
- Internal Positive Control (IPC)
- An exogenous DNA template of known sequence and concentration added to the PCR reaction alongside the forensic sample. If the IPC fails...
- Mini-STR
- A PCR assay in which both primers sit within a few base pairs of the STR repeat, producing amplicons as short as...
- Ministr (Reduced-Size) STR
- A short tandem repeat assay redesigned so that the amplicon spans a shorter distance from primer to primer, typically less than 200...
- PCR Inhibitor
- A co-extracted substance that interferes with Taq polymerase activity or primer annealing. Common inhibitors in forensic samples include haemoglobin (from blood on...
- Taq Polymerase
- Thermostable DNA polymerase from Thermus aquaticus, the enzyme that makes PCR practical. Stable at 95°C, it extends primers in the 5'-to-3' direction...
Explained in these topics
- DNA Degradation: Mechanisms, Inhibitors and Environmental Effects
- DNA, RNA and the Central Dogma of Molecular BiologyHydrolytic loss of a purine base (adenine or guanine) from the deoxyribose sugar, creating an abasic site that blocks DNA polymerase extension. One of the prim...