Protein removal and DNA purification

This is another important step in the ChIP-exo protocol. The aim of this step is to discard any unwanted biomolecule, such as proteins and RNA, to have a DNA solution as purer as possible and to create a library of DNA sequences that can be later sequenced in order to identify the target sequence where the transcription factor was bound. Three main reagents are used in this step:

• Tris EDTA buffer: This is a common buffer used to solubilize DNA samples. It's really important not to forget this step since this buffer will protect the DNA from further degradation thanks to the presence of EDTA, which chelates ions that are involved in DNA degradation processes.

• Protease K: This enzyme will degrade the remaining transcription factors present in the solution.

• RNase: This enzyme will degrade the remaining RNA molecules present in the sample.