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Table 1 Ancient DNA damage

From: Ancient DNA studies: new perspectives on old samples

Damage Type of process Effects on DNA molecule Possible solutions in aDNA classical sequencing methodologies
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
  1. UNG : Uracil-N-glycosylase; Spex: Single Primer Extension; PTB: N-phenylacyl thiazolium bromide.
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