Addition of a topoisomerase greatly facilitates nucleosome association with cccDNA.

When a topoisomerase is present during nucleosome assembly, it cannot act on the DNA bound to the nucleosome. Instead, the topoisomerase relaxes the DNA not included in nucleosomes, reducing the positive superhelical density in these regions by decreasing the linking number.

TLS Online TPP Program

#Id: 6125

#Unit 3. Fundamental Processes

Humans have the enzyme hSMUG1, which removes any U residues that occur in single-stranded DNA during replication or transcription.  Two other human DNA glycosylases, TDG and MBD4, remove either U or T residues paired with G, generated by deamination of cytosine or 5-methylcytosine, respectively.

TLS Online TPP Program

#Id: 6126

#Unit 3. Fundamental Processes

DNA glycosylases recognize and remove formamidopyrimidine and 8-hydroxyguanine (both arising from purine oxidation), hypoxanthine (arising from adenine deamination), and alkylated bases such as 3-methyladenine and 7-methylguanine.

TLS Online TPP Program

#Id: 6127

#Unit 3. Fundamental Processes

Enzymes that remove bases from DNA are called glycosylases and lyases

TLS Online TPP Program

#Id: 6128

#Unit 3. Fundamental Processes

Glycosylase action is followed by the endonuclease APE1, which cleaves the polynucleotide chain on the 5’ side. This in turn attracts a replication complex including the DNA polymerase d/E and ancillary components, which performs a short synthesis reaction extending for two to 10 nucleotides. The displaced material is removed by the endonuclease FEN1.

TLS Online TPP Program

#Id: 6129

#Unit 3. Fundamental Processes

When the initial removal involves lyase action, the endonuclease APE1 instead recruits DNA polymerase b to replace a single nucleotide. The nick is then sealed by the ligase XRCC1/ligase-3. This is called the short-patch pathway.

TLS Online TPP Program

#Id: 6130

#Unit 3. Fundamental Processes

Alkyladenine DNA glycosylase (AAG), recognizes and removes a variety of alkylated substrates, including 3-methyladenine, 7-methylguanine, and hypoxanthine.