Figure 6.

Ancient DNA damage: a profile. After depurination (step 1), internal AP-sites are subject to β-elimination (arrow, step 2), which opens the phosphodiester bond mainly for 3′ of AP-sites. In addition, DNA strands are subject to single-strand breaks. As a result of terminal transferase preference for 3′-hydroxy ends, most abasic sites located 3′ of the aDNA fragment will not be poly(A) tailed, unless the nucleotidic sugar is further degraded. Such termini are not represented, albeit they are likely to represent a significant fraction of aDNA templates. Cytosine deamination in uracils occurs much faster on single-stranded parts of DNA (step 3) and results in increased G→A misincorporation rates at the beginning of Helicos sequence reads. Other types of damages, such as interstrand cross-links, which affect aDNA molecules (and hamper further sequence characterization), are not reported.