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3 Formation of DNA Lesions, its Prevention and Repair
Although a plethora of different lesions are formed in living cells every day,
under normal conditions, majority of cells remain disease free. This is due to the
fact that living cells have complex defense mechanisms operating against cell alterations mediated by reactive species. The main components of these defence
mechanisms include several anti-oxidants which can be classified into enzymatic
and non-enzymatic categories [29, 30]. Enzymatic anti-oxidants such as superoxide dismutase (SOD), catalase, glutathione, glutathione peroxidase and reductase in
general inhibit the formation of reactive species in cells [31] while non-enzymatic
anti-oxidants like vitamin E (α-tocopherol), vitamin C (ascorbic acid), carotenoids,
flavonoids etc. scavenge the reactive species. These anti-oxidants ensure that there
is minimal damage to DNA and other cellular components. The other and most important mechanism of cellular defense involves direct repair of the damaged bases
[32–34] or their excision out of DNA followed by insertion of a new appropriate
base at the corresponding location [35, 36]. This function is basically performed
by different proteins that have inherent catalytic abilities. Biological systems have
evolved with many such enzymes that have specific repair functions. For example,
oxidative DNA base lesions are repaired by DNA glycosylases while alkylated base
lesions are repaired by DNA alkyl transferases. The enzymatic DNA repair pathways have been shown to consist of two important processes i.e. damage recognition and catalysis.
Due to a spectrum of DNA damage lesions produced in cells, multiple cellular
defense mechanisms are sometimes unable to prevent and repair these lesions. As a
consequence, cells get affected by diseases. Therefore, understanding of formation
of different biochemical reaction intermediates and products and multiple functions
of various cellular defense mechanisms will certainly enrich our knowledge which
can enable us to devise techniques to protect cells from diseases, e.g. by designing
appropriate drugs. Application of theoretical methods can be immensely valuable
towards understanding molecular mechanisms involved in the functioning of DNA,
anti-oxidants and proteins. It is established that use of density functional theory
(DFT) and molecular dynamics simulation can greatly help in the pursuit of explaining structures and functions of different biomolecules. For relatively smaller
molecules, DFT calculations can predict structures and even reaction energetics
fairly accurately. Therefore, we will mainly discuss results of DFT studies regarding
mechanisms of formation of different DNA base lesions, action of anti-oxidants and
repair of different base lesions in DNA by enzymes.
3.2 Endogenous Formation of Reactive Species
It is established that during the normal metabolic activities, some electrons (1–3 %
of the total number) leak away from the mitochondrial electron transport chain and
get bound to normal molecular oxygen, producing superoxide radical anion (O 2
•−
)
[37, 38]. Electrons also leak from enzymatic sources such as NAD(P)H and xan-
3 Formation of DNA Lesions, its Prevention and Repair
Although a plethora of different lesions are formed in living cells every day,
under normal conditions, majority of cells remain disease free. This is due to the
fact that living cells have complex defense mechanisms operating against cell alterations mediated by reactive species. The main components of these defence
mechanisms include several anti-oxidants which can be classified into enzymatic
and non-enzymatic categories [29, 30]. Enzymatic anti-oxidants such as superoxide dismutase (SOD), catalase, glutathione, glutathione peroxidase and reductase in
general inhibit the formation of reactive species in cells [31] while non-enzymatic
anti-oxidants like vitamin E (α-tocopherol), vitamin C (ascorbic acid), carotenoids,
flavonoids etc. scavenge the reactive species. These anti-oxidants ensure that there
is minimal damage to DNA and other cellular components. The other and most important mechanism of cellular defense involves direct repair of the damaged bases
[32–34] or their excision out of DNA followed by insertion of a new appropriate
base at the corresponding location [35, 36]. This function is basically performed
by different proteins that have inherent catalytic abilities. Biological systems have
evolved with many such enzymes that have specific repair functions. For example,
oxidative DNA base lesions are repaired by DNA glycosylases while alkylated base
lesions are repaired by DNA alkyl transferases. The enzymatic DNA repair pathways have been shown to consist of two important processes i.e. damage recognition and catalysis.
Due to a spectrum of DNA damage lesions produced in cells, multiple cellular
defense mechanisms are sometimes unable to prevent and repair these lesions. As a
consequence, cells get affected by diseases. Therefore, understanding of formation
of different biochemical reaction intermediates and products and multiple functions
of various cellular defense mechanisms will certainly enrich our knowledge which
can enable us to devise techniques to protect cells from diseases, e.g. by designing
appropriate drugs. Application of theoretical methods can be immensely valuable
towards understanding molecular mechanisms involved in the functioning of DNA,
anti-oxidants and proteins. It is established that use of density functional theory
(DFT) and molecular dynamics simulation can greatly help in the pursuit of explaining structures and functions of different biomolecules. For relatively smaller
molecules, DFT calculations can predict structures and even reaction energetics
fairly accurately. Therefore, we will mainly discuss results of DFT studies regarding
mechanisms of formation of different DNA base lesions, action of anti-oxidants and
repair of different base lesions in DNA by enzymes.
3.2 Endogenous Formation of Reactive Species
It is established that during the normal metabolic activities, some electrons (1–3 %
of the total number) leak away from the mitochondrial electron transport chain and
get bound to normal molecular oxygen, producing superoxide radical anion (O 2
•−
)
[37, 38]. Electrons also leak from enzymatic sources such as NAD(P)H and xan-