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Lesion (in)tolerance reveals insights into DNA replication fidelity
Eva Freisinger1, Arthur P Grollman, Holly Miller
1Department of Pharmacological Sciences, Center for Structural Biology, SUNY at Stony Brook, Stony Brook, NY, USA.
The EMBO Journal
|April 2, 2004
Summary
DNA polymerases encounter DNA lesions, determining repair pathways. Crystal structures reveal how RB69 polymerase interacts with abasic sites and 8-oxodG lesions, clarifying DNA synthesis barriers and fidelity mechanisms.
Area of Science:
- Molecular Biology
- Structural Biology
- Biochemistry
Background:
- DNA replication encounters unrepaired DNA lesions, influencing damage avoidance pathways.
- The interaction with replicative DNA polymerases dictates error-prone or error-free lesion bypass.
- Understanding these interactions at the atomic level is crucial for DNA repair and fidelity.
Purpose of the Study:
- To determine the crystal structures of RB69 DNA polymerase complexed with DNA containing abasic sites and 8-oxoguanosine (8-oxodG) lesions.
- To elucidate the atomic details of DNA polymerase interactions with damaged nucleotides.
- To gain insight into the mechanisms of DNA synthesis past lesions and polymerase fidelity.
Main Methods:
- X-ray crystallography was used to determine the structures of RB69 DNA polymerase.
- Complexes were formed with DNA templates containing specific premutagenic lesions: abasic site and 8-oxodG.
- Structural analysis focused on active site interactions and conformational changes.
Main Results:
- A novel, open, catalytically inactive conformation of RB69 DNA polymerase was observed with a primed abasic site template.
- This structure provides the first molecular insight into the DNA synthesis barrier posed by abasic sites.
- The ternary complex of 8-oxodG:dCTP with the polymerase closely resembles the replicating complex with undamaged DNA, explaining facile bypass.
Conclusions:
- The study reveals distinct structural mechanisms for bypassing different DNA lesions.
- The abasic site presents a significant barrier, inducing a catalytically inactive polymerase conformation.
- The 8-oxodG lesion is bypassed with relative ease and fidelity due to structural similarity to normal replication.