83
3 Formation of DNA Lesions, its Prevention and Repair
site, leaving a 5’-phosphate and a 3’-α,β-unsaturated aldehyde [208] (Fig. 3.10b).
Subsequently, a new nucleotide is synthesized by DNA polymerase β to be placed
in the vacant position in DNA which then gets sealed to the nearest backbone by a
DNA ligase [208].
As described above, catalysis by DNA glycosylases involves the dissociation
of the N-glycosidic bond which can be achieved by its hydrolysis [208]. Generally
a nucleophile located proximal to the glycosidic bond helps in the hydrolysis of
the glycosidic bond [227]. After N-glycosidic bond dissociation, the corresponding
base carries an extra electron which needs to be stabilized by an acid. It has been
shown that in the case of monofunctional DNA glycosylases [228], a water molecule acts as a nucleophile leading to hydrolysis of the glycosidic bond. However,
in the case of bifunctional glycosylases, an amino acid residue of the enzyme acts as
the necessary nucleophile [208, 210, 212, 224, 225]. Other amino acids that directly
or indirectly (through water mediated hydrogen bonds) stabilize the transition states
of the glycosidic bond cleavage reaction are of paramount importance in reducing
the barrier energy. As proposed earlier, a complete glycosidic bond cleavage may
occur in multiple steps depending on the enzyme and the affected DNA base. In addition to this, processing of the phosphate and sugar moieties previously attached to
the affected base also occurs in multiple steps and ultimately the DNA polymer gets
sealed by completing the repair process [208, 210, 212, 224, 225].
The enzyme adenine DNA glycosylase which is also known as MutY catalyzes
base excision repair by removing adenine from the abnormal base pair between
2′-deoxyadenosine and 8-oxo-2′-deoxyguanosine. In their study, McCann and Berti
[228] studied the crystal structure of Escherichia coli MutY, obtained the transition
state structures of MutY catalyzed DNA hydrolysis and also computed energetics
of the reaction mechanism employing B3PW91/6-31þG(d, p) level of density functional theory. Gibbs free energy changes involved in the reaction mechanism proposed by McCann and Berti [228] were calculated at the MP2/AUG-cc-pVDZ level
of theory in the gas phase using the B3LYP/6-31G(d, p) level optimized geometries
[228]. It was found that in the model proposed by McCann and Berti [228], the
second barrier energy was too high to be overcome in the biological medium. This
difficulty was resolved by showing that the formation of the product having dissociated N-glycosidic bond of 2′-deoxyadenosine from the intermediate formed after
the first step which has a moderate barrier energy would occur directly and barrierlessly without involving any other step [229]. This example shows that detailed
quantum chemical studies of reactions can be immensely valuable to investigate
mechanisms operating in complex biological systems.
Acknowledgment PCM is thankful to the University Grants Commission (New Delhi) for financial support. NRJ is thankful to the Indian National Science Academy (INSA) for Indo-Australia
early career visiting fellowship. NA gratefully acknowledges use of facilities of the Department of
Chemistry, University of Saskatchewan, Canada.
3 Formation of DNA Lesions, its Prevention and Repair
site, leaving a 5’-phosphate and a 3’-α,β-unsaturated aldehyde [208] (Fig. 3.10b).
Subsequently, a new nucleotide is synthesized by DNA polymerase β to be placed
in the vacant position in DNA which then gets sealed to the nearest backbone by a
DNA ligase [208].
As described above, catalysis by DNA glycosylases involves the dissociation
of the N-glycosidic bond which can be achieved by its hydrolysis [208]. Generally
a nucleophile located proximal to the glycosidic bond helps in the hydrolysis of
the glycosidic bond [227]. After N-glycosidic bond dissociation, the corresponding
base carries an extra electron which needs to be stabilized by an acid. It has been
shown that in the case of monofunctional DNA glycosylases [228], a water molecule acts as a nucleophile leading to hydrolysis of the glycosidic bond. However,
in the case of bifunctional glycosylases, an amino acid residue of the enzyme acts as
the necessary nucleophile [208, 210, 212, 224, 225]. Other amino acids that directly
or indirectly (through water mediated hydrogen bonds) stabilize the transition states
of the glycosidic bond cleavage reaction are of paramount importance in reducing
the barrier energy. As proposed earlier, a complete glycosidic bond cleavage may
occur in multiple steps depending on the enzyme and the affected DNA base. In addition to this, processing of the phosphate and sugar moieties previously attached to
the affected base also occurs in multiple steps and ultimately the DNA polymer gets
sealed by completing the repair process [208, 210, 212, 224, 225].
The enzyme adenine DNA glycosylase which is also known as MutY catalyzes
base excision repair by removing adenine from the abnormal base pair between
2′-deoxyadenosine and 8-oxo-2′-deoxyguanosine. In their study, McCann and Berti
[228] studied the crystal structure of Escherichia coli MutY, obtained the transition
state structures of MutY catalyzed DNA hydrolysis and also computed energetics
of the reaction mechanism employing B3PW91/6-31þG(d, p) level of density functional theory. Gibbs free energy changes involved in the reaction mechanism proposed by McCann and Berti [228] were calculated at the MP2/AUG-cc-pVDZ level
of theory in the gas phase using the B3LYP/6-31G(d, p) level optimized geometries
[228]. It was found that in the model proposed by McCann and Berti [228], the
second barrier energy was too high to be overcome in the biological medium. This
difficulty was resolved by showing that the formation of the product having dissociated N-glycosidic bond of 2′-deoxyadenosine from the intermediate formed after
the first step which has a moderate barrier energy would occur directly and barrierlessly without involving any other step [229]. This example shows that detailed
quantum chemical studies of reactions can be immensely valuable to investigate
mechanisms operating in complex biological systems.
Acknowledgment PCM is thankful to the University Grants Commission (New Delhi) for financial support. NRJ is thankful to the Indian National Science Academy (INSA) for Indo-Australia
early career visiting fellowship. NA gratefully acknowledges use of facilities of the Department of
Chemistry, University of Saskatchewan, Canada.