Nucleophilic sites on DNA

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Nucleophilic sites on DNA
Almost all N and O sites are capable of being
alkylated by a strong enough electrophile
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Other considerations

• Accessibility of electrophile to sites in major
  and minor groove
• Eg. N-7 of G is accessible in major groove of
  B-DNA

3
World-War I and II nerve gases
See Problem 5
Bifunctional alkylating agents
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5
Can be fixed by repair enzymes
Strand cleavage
E1cb elimination
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Nitrosoureas
R CH3 antitumour activity R CH2CH2Cl used
in brain tumour therapy
Isocyanic acid Carbamoylating agent
Methyl diazonium, potent methylating agent
7
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Cis-platin
Ligand exchange reaction (not alkylation)
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Intra-strand crosslinks N7-G gt N7-A
Cis isomer has anti-tumour activity
Inter-strand crosslinks but NO anti-tumour
activity
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Bisulfite deamination of C to U
Bisulfite is found as a food preservative
uracil
cytosine
C to U transition is potentially mutagenic
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Methylation of cytosine by methylase enzymes
5-methyl C
Carried out by bacteria to protect self DNA from
being cleaved by bacterial restriction enzymes
DNA methylation affects gene expression
(silencing)
Enzymes that methylate flip out base in active
site
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3 Modes of small molecule interaction with DNA
Electrostatic surface interaction eg Na Mg,
polyamines
Intercalation between base-pairs
Minor groove binding
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Intercalation of Daunomycin into (CGTACG)2
Helix unwound 10-30
Major groove is opened
Planar rings inserted in between base-pairs
p-p interactions, hydrophobic effect
Prefer to stack 5- to a G residue
Take up the same space as a base-pair (3.4)
Non-aromatic bits dangle into minor groove
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Intercalators are extended aromatic (p) systems
Antitumour agent (DNA topoisomerase I)
antimalarials
Antibacterial agent (DNA topoisomerase II)
Also cause DNA cleavage
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Topoisomerases
Catalyse unwinding of supercoiled DNA (packaged)
ready for replication
Topo I gives 3-OH
Topo II Gives 5-OH
Transient DNA break allows unwinding
Intercalators trap DNA-drug-Topoisomerase complex