Figure 1.

Predicted activity of UDG and endoVIII in 454 library preparation of ancient DNA. T4 PNK phosphorylates 5′-ends leaving 5′-phosphate groups. UDG removes uracils, which are concentrated in short 5′- and 3′-overhangs in ancient DNA, leaving abasic sites. EndoVIII then cleaves on both sides of the abasic sites, leaving 5′- and 3′-phosphate groups. T4 polymerase fills in remaining 5′-overhangs and chews back 3′-overhangs, possibly aided by the 3′-phosphatase activity of PNK. Blunt-end ligation and fill-in of sequencing adaptors can then take place.