Table 2.

Various types of ancient DNA damage (from [4, 17] with modifications).

Type of damage	Cause of damage	Effect on DNA	Possible solution
Nucleobases and deoxyribose degradation	Postmortem destruction by intracellular nucleases, degradation by microorganisms and other chemical processes	Apurinization of DNA, strand breaks, decrease of DNA fragment size, decrease of the overall amount of DNA	Amplification of short (<100-200 bp) overlapping fragments
Cross-links which block PCR	Alkylation, Maillard reaction (chemical reaction between a sugar molecule and an amino group of a nucleobase or an amino acid)	Cross-links between DNA strands in a single molecule; cross-links between DNA strands of different molecules; or cross-links between DNA and proteins	Treating the sample with reagents that destroy cross-links
Deamination and other types of oxidative or hydrolytic DNA base modifications	Adenine → hypoxanthine Guanine → xanthine Cytosine → uracil 5-methyl-cytosine → thymine	Insertion during amplification of nucleotides that were not present in the original nonmodified template	Treatment by DNA uracil-N-glycosylase, which removes cytosine deamination products. Determination of a consensus sequence based on multiple sequencing of the analyzed regions: Multiple independent PCR, cloning of the original template or PCR products, and sequencing of several clones