Ancient Dna: Methods And Protocols -

To handle chemical damage, researchers may use Uracil-DNA-Glycosylase (UDG) to remove uracil bases, reducing sequencing errors, though this can sometimes shorten already tiny fragments.

Synthetic DNA "adapters" are attached to the ends of the fragments, allowing them to bind to the sequencing platform.

Proteinase K is added to break down cellular proteins and nucleases.

Deamination (the conversion of cytosine to uracil) occurs frequently at the ends of fragments, leading to sequencing errors (C-to-T transitions).

Modern DNA from researchers or the environment is "fresher" and more intact than aDNA, making it easy for a tiny amount of modern DNA to overwhelm the ancient sample. 2. Sample Selection and Preparation

The silica-based extraction method is the industry standard. DNA binds to silica in the presence of high concentrations of chaotic salts, allowing impurities to be washed away before the DNA is eluted into a clean buffer. 4. Library Preparation and Sequencing