Instructor: Dr. Natalia Tretyakova, Ph.D. «hyperlink ""»    -   6-3432
PDB reference correction and design Dr.chem., Ph.D. Aris Kaksis, Associate Prof. e-mail:
Fidelity of Polymerization: Absolutely Essential !!
Error Probability = Polymerization error   10-4  
                                 3'--> 5' Nuclease error   10-3   
                                                                   = 10-7 or 1 in 10,000,000
DNA Synthesis: addition of new dNTPs follows Watson-Crick rules
                          G = C                                                             A= 
Polymerase errors
Very low rate of misincorporation (1 per 108)
  Errors can occur due to the presence of minor tautomers of nucleobases.

                          = A                            Cytosine C = A      Rare tautomer of A
Normal base pairing                                                                  Mispairing
                                                                          Types of DNA Mutations
1.         Point mutations: substitution of one base pair for another, e.g. A for GC
• the most common form of mutation
transition;         purine to purine and             pyrimidine to pyrimidine
transversions;    purine to pyrimidine or        pyrimidine to purine
2.         Deletion of one or more base pairs 
3.         Insertion of one or more base pairs
Termination of Polymerization: The Key to Nucleoside Drugs
AZT                                        Ziagen                                                                   Acyclovir
Normal base pairing in DNA and
an example of mispairing via chemically modified nucleobase

                   Adenine         A=               O6-Alkyl-Guuanine   
            Guanine              G = C Cytosine


Chemical Mutagens
              Mutations can occur when the normal bases that are incorporated are changed.
1. Base analogs or bases that have altered hydrogen bonding capabilities can cause transitions.
          Ex. Bromo and Guanine or 2-aminopurine and cytosine
2. Bases can be modified on the DNA by mutagens.
adenine is oxidatively deaminated to hypoxanthine, cytosine to , guanine to xanthine
3. Intercalating Agents • insertion and deletion mutants
           Cytosine Deamination
                                                                       DNA Damage
Base pairs can be damaged by
                   environment or chemical factors, such as UV light or nitrosureas .

1. Pyrimidine dimers due to UV light
repaired by excision of the region by uvrABC excinuclease followed by gap filling by DNA Pol I.
• can be repaired by photolyase, which splits the dimers
• cause of xeroderma pigmentosum, don't have excinuclease
2. Nitrosoureas and other alkylating agents are obtained from smoking and other chemical contaminants.
• result in methylation of G to form O6Methyl G, which base pairs with T and T to form
                          O4Methyl T, which base pairs with G     there are some demethylation enzymes
3. Cytosine deamination to Uracil
• spontaneous
uracil-DNA glycosidase, AP exonuclease, DNA Pol I.
4. DNA repair is based on methylation of parental strand and a mismatch repair system that
                                                                                                                replaces the incorrectly incorporated base.
        DNA Synthesis: Take Home Message
1) DNA synthesis is carried out by DNA polymerases with high fidelity.
2) DNA synthesis is characterized by initiation,
                          priming and processive synthesis steps and proceeds in 5’
--> 3’ direction.
3) Modifications of DNA base pairs, if not repaired, can lead to mutations
of the DNA sequence.