Table 1 Ancient DNA damage

Oxidative damage

Formation of strand breaks (single-stranded nicks)

Cleavage of the phosphodiester backbone

PCR of overlapping fragments of short length

Depurination resulting in a baseless site

Multiple independent PCR Cloning and sequencing of several clones

Breakage of the sugar backbone through b-elimination

Uracil-N-glycolase treatment

Results in lesions blocking the polymerase enzyme, and promoting chimeric sequences through ‘jumping’ PCR

Blocking primers Single primer extension or Spex

Degradation by microorganisms’ nucleases in the post mortem cell

Strand breaks

Short fragment length

PCR of overlapping fragments of short length

DNA crosslinks

Inter-strand crosslinks by alkylation

May prevent the amplification of endogenous template molecules

PTB (N-phenylacyl thiazolium bromide)

Intermolecular crosslinks by Maillard reaction

Increases the risk of contamination

Hydrolysis damage

Results in miscoding lesions, for example, deamination of cytosine and adenine to uracil and hypoxathine, respectively

Results in the incorporation of erroneous bases during amplification and change of coding

Multiple independent PCR Cloning and sequencing of several clones UNG treatment