DNA damage (M.B+G)

lecture 3

sources of DNA damage along DNA molecules

environment, medical, lifestyle

places DNA damage can occur

• damage in bases → modification of base chemistry→ point mutations

• damage to phosphate deoxyribose backbone → DNA breakage (one or both strands) → insertions, deletions, translocations

different types of DNA mutations

• point mutations (transitions + transversions- substitution + replacement)

• Insertion

• deletion

• silent

• missense (conservative + non-conservative)

• frame-shift

• nonsense

mutation on genetic code result in which mutations

 Silent,

Missense,

Nonsense

Frame-Shift mutations

transition point mutation vs transversion point mutation

- transitions: substitution change from purine to -purine or pyrimidine to pyrimidine base

- transversions = substitution change from purine to- pyrimidine base

missense mutation types

conservative= single base substitution mutation resulting in sub of original amino acid (a.a) w/ one that is chemically similar (e.g both original and replacement are negtively charged)

- nonconservative= single base substitution mutation resulting in sub of original amino acid (a.a) w/ one that is chemically dissimilar (e.g both original is negative charged and replacement are positively charged)

which mutations can cause frame-shift

insertion, deletion, duplication

somatic DNA mutations

Somatic mutations: mutations that occur after zygote formation and are not genetically inherited.

• Some somatic mutations alter genes that can regulate cell survival, division and apoptosis leading to uncontrolled cell growth

different types of DNA damage

• base pair mis-match: consequence of nucleotide mismatch during DNA replication not repaired

• abnormal base pairs: caused by deamination. Abnormal base pairs (such as with the uracil nucleotide) can also lead to abasic sites in a bid to fix the abnormality

• abasic site: caused by depurination. process not repaired can lead to loss of nucleotide pair

• Uv-induced thymine dimers

• DNA alkylation

• DNA oxidation via ROS

deamination

deamination= removal of NH3 from a base

depurination

depurination= spontaneous loss of a purine base (A or G) from DNA

UV- induced thymine dimers

two thymine bases sitting next to each other form a covalent bond, due to energy absorbed from UV light

- makes a little “ring” structure (a cyclobutane ring).

- It bends or twists the DNA helix shape so it can’t be read or copied properly.

- When DNA is damaged like this:

- The cell’s DNA-copying machinery (the replication fork) can’t move past the distortion.

- If not repaired, it can cause mutations or even double-strand breaks.

- also known as Cyclobutane Pyrimidine Dimers (CPDs)

DNA alkylation

alkylating agents (eg- **ethylmethane sulfonate**, or EMS) adds an alkyl group (–CH₃ or –CH₂CH₃) to parts of the DNA bases.

- The most common places this happens are:

- O⁶ position of guanine (G)

- O⁴ position of thymine (T)

- When guanine gets modified at O⁶, it’s now O⁶-alkylguanine (for example, O⁶-ethylguanine).

- This modified G can no longer pair correctly with cytosine (C).

- Instead, it mistakenly pairs with thymine (T) during DNA replication.

- This changes the original G–C pair into an A–T pair

- That’s called a transition mutation (G→A or C→T)

- Alkylation doesn’t break the DNA strand, but it changes its code.

- These wrong base pairings cause transition mutations if not repaired.

DNA oxidation via ROS

due to reactive oxygen species

- When ROS hits guanine, it changes its chemical structure, creating damaged versions of it.

- can hit other DNA bases, but Guanine is the easiest due to its' lowest ionising potential

- There are two common ones:

1. 8-hydroxyguanine (8-oxoG) Also called *8-oxoguanine**.

- This is the most common oxidation product.

- It still looks a bit like guanine, but it pairs with adenine (A) instead of cytosine (C)!

- So when DNA replicates, it causes a G→T (or C→A) mutation.

2. 2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy-G)

- think of this as a more broken-down version of guanine.

- It also disrupts normal base pairing and can stall replication or cause mutations.

- Oxidative DNA damage doesn’t break the DNA strand right away.

- But it changes base-pairing rules, so during DNA replication, the wrong bases get added.

- Over time, this causes mutations, which can lead to aging, cell malfunction, or even cancer if not repaired.