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Exploring Cycloreversion Reaction of Cyclobutane Pyrimidine Dimers Quantum Mechanically
Donglian Huang1, Shanfeng Chen1, Jingzhi Pu2
1School of Chemistry and Chemical Engineering , Guangxi University for Nationalities , 188 Daxue East Road , Nanning , Guangxi 530006 , China.
The Journal of Physical Chemistry. A
|February 19, 2019
Summary
The study reveals that cyclobutane pyrimidine dimer (CPD) DNA repair primarily involves a stepwise splitting of the CPD radical anion. Protonation by adjacent residues stabilizes the anion but does not accelerate the ring-opening process.
Area of Science:
- Biochemistry
- Photochemistry
- Computational Chemistry
Background:
- Cyclobutane pyrimidine dimers (CPDs) are major DNA lesions caused by UV light.
- DNA photolyase repairs CPDs using UV light and cofactors.
- The role of protonation in CPD repair remains unclear.
Purpose of the Study:
- To investigate the mechanism of CPD repair.
- To determine if protonation of CPD is involved in DNA repair.
- To explore cycloreversion reactions and proton transfers in CPD models.
Main Methods:
- Quantum mechanical calculations were employed.
- Potential energy surface maps were computed in vacuum and water.
- One-dimensional potential energy profiles for proton transfer were calculated.
Main Results:
- The most likely repair mechanism involves stepwise splitting of the CPD radical anion (CPD•2-).
- The C5-C5' bond splits first, followed by the C6-C6' bond.
- Free energies of activation for these steps are low (0.9 and 3.1 kcal/mol).
Conclusions:
- CPD repair likely proceeds via sequential bond cleavage of the CPD radical anion.
- Adjacent Glu283 can stabilize the CPD radical anion via hydrogen bonding, potentially increasing quantum yield.
- Protonation of the CPD radical anion by Glu283 does not accelerate the ring-opening rate.
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