MUTATIONS AND REPAIR MECHANISMS FOR NUCLEIC ACIDS - handout

Mutations
- mutations are caused by errors in DNA replication
Types of mutations:
1. Point mutation – mutations that reflect a single base change
 Silent / neutral – change in base, but mutated codon will result in the same aa
 Missense – change in base will code for different aa
 Nonsense – change in base will code for stop codon
EXAMPLES:
Normal codon: UAU [tyrosine]
Silent / neutral: UAC [tyrosine]
Missense: UCU [serine]
Nonsense: UAG [stop]

2. Deletion – mutations that will remove a codon

3. Insertion – mutations that will add a codon
4. Frameshift – mutation that will change how the mRNA sequence is translated
 Frameshift addition – adding a base will shift the coding sequence
 Frameshift deletion – deleting a base will shift the coding sequence
EXAMPLES:
Normal gene sequence will code: “THE BIG MEN ARE FUN NOW”
Point mutation: “THE BIG MEN ATE FUN NOW”
Deletion: “THE BIG MEN FUN NOW”
Insertion: “THE BIG MEN ARE TOO FUN NOW”
Frameshift addition: “THE BIG MEN ATR EFU NNO W”
Frameshift deletion: “THE BIG MEN AEF UNN OW”

Effects of Mutations:
1. Transition effect – mutation is a change from
a. purine  purine (A  G or G  A)
b. pyrimidine  pyrimidine (C  U or U  C)
2. Transversion effect – mutation is a change from
a. purine  pyrimidine (AU or C; GU or C)
b. pyrimidine  purine (CA or G; U A or G)

Spontaneous Mutations – mutations that occur due to polymerase errors

1. Tautomeric base mispair
- “rare” forms of the amino acids (imino- form or keto- form) will allow H-bonding of non-
complementary bases
e.g. (A can bond with imino form of C; T can bond with keto form of G)
2. Simple misalignment
- sequence not in a “straight line”; polymerase skips a base
3. Palindromic misalignment
- inverted repeats that induce a hairpin loop
4. Repetitive sequence misalignment
- multiple consecutive sequences are “skimmed” through by the polymerase, leading to error

mdliu/csmadarang 2017
Induced Mutations – mutations that occur through physical or chemical mutagens
Reactivity of bases (least to greatest): A  G  C  T
1. Thymine dimers form in the presence of UV light
 Two thymine bases next to each other will bind together instead of binding with a
complementary base, leading to a kink in the DNA strand
2. Guanine reactivity to the presence of high concentration of H2O
 In high enough concentration, the introduction of water to the DNA strand can release
guanine from the nucleotide, resulting in a sugar-phosphate backbone without the
guanine base
3. Heat
 Enough heat will cause denaturation of the strands, forming apurinic/apyrimidinic sites
(AP sites) which result in a sugar-phosphate backbone without the respective base
4. Ionizing radiation
 Exposure to radiation will cause formation of free radicals which can damage DNA in
continuous free radical propagation
Chemical Mutagens:
5. Cigarette Smoke Condensate (CSC)
 Free radical of the alkoxy group will lead to thymine dimerization
6. Polycyclic Aromatic Hydrocarbons (PAH)
 Acts as an intercalating agent –
 Intercalating agent can distort DNA structure to prevent replication (i.e. changing DNA
structure to prevent enzymes from acting on it)
7. Other intercalating agents
 Caffeine, alcohol, moldy food (aflatoxin B), hydroxylamine

Repair Mechanism
- DNA must have mechanisms to keep the integrity of the genetic code and prevent mutations from
occurring in future generations.
- DNA Pol I 5’ 3’ exonuclease activity reads the errors, the DNA Pol I 3’  5’ exonuclease activity
removes erroneous nucleotides.

1. Nick translation – DNA Polymerase I can use 5’ 3’ exonuclease activity to remove RNA primers and
DNA errors using the cut-and-patch method

2. Mismatch repair – enzyme recognition of incorrect base pairs will remove the incorrect base pair and
replicate with a new base pair. [chapter 10, figure 10.16].

3. Base excision repair – DNA glycosylase removes a damaged base leaving an AP site (apurinic or
apyrmidinic site; depending on the base lost). The AP site is acted upon by AP endonuclease for removal
of the sugar and phosphate. Excision exonuclease removes bases next to the AP site, until DNA
polymerase comes in to fill the gap [chapter 10, figure 10.17].

4. Nucleotide-excision repair – this repair mechanism fixes structural errors in DNA. When a lesion
(structural errors) are detected, a small section including the lesion is removed by ABC excinuclease.
DNA polymerase and DNA ligase then come in to fill the gap after removal [chapter 10, figure 10.18].

mdliu/csmadarang 2017