Abasic Site
Definition
A position in the DNA backbone where the nitrogenous base has been lost, leaving only the deoxyribose-phosphate scaffold. Also called an AP (apurinic/apyrimidinic) site. Abasic sites block most DNA polymerases and are chemically labile, breaking the backbone under alkaline conditions.
- Also called
- AP (apurinic/apyrimidinic) site
- Cause
- Loss of the nitrogenous base
- Effect on replication
- Blocks most DNA polymerases
- Chemical property
- Labile, breaks under alkaline conditions
Common questions
How does an abasic site affect PCR-based DNA typing?+
Because it blocks most polymerases from extending past it, template molecules carrying abasic sites often fail to amplify, contributing to allele dropout or reduced yield, an effect that becomes more significant in degraded evidentiary samples.
Is an abasic site the same as a base substitution?+
No. A substitution swaps one base for a different one, while an abasic site has no base at all at that position, leaving only the sugar-phosphate backbone.
Related terms
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- An oxidised form of guanine produced by reactive oxygen species attacking the C8 position of the guanine ring. 8-Oxoguanine mispairs with adenine...
- Depurination
- Hydrolytic cleavage of the N-glycosidic bond between deoxyribose and a purine base (adenine or guanine), generating an abasic (apurinic) site. Abasic sites...
- 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...
- 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...