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DNA Repair
Mechanisms

How cells detect and fix damaged DNA to preserve genomic integrity: Base Excision Repair, Nucleotide Excision Repair, and Mismatch Repair.

Biochemistry

Why DNA Repair Matters

Every cell in your body faces an estimated 10,000 to 100,000 DNA lesions per day: oxidative damage, deamination, replication errors, UV-induced photoproducts, and more. Without robust repair systems, mutations accumulate, leading to cancer, premature aging, and cell death.

Types of DNA Damage

Small Base Lesions
Oxidized bases (8-oxoG), deaminated bases (uracil from cytosine), alkylated bases: subtle, single-base chemical changes.
Bulky Adducts
UV-induced thymine dimers (CPDs), benzo[a]pyrene-guanine adducts: large, helix-distorting modifications that block replication.
Replication Errors
Misincorporated bases and insertion/deletion loops (IDLs) that escape polymerase proofreading: the base is normal but mispaired.

Three Core Pathways

BER Base Excision Repair Small base lesions NER Nucleotide Excision Repair Bulky helix-distorting MMR Mismatch Repair Replication errors Common Core Steps Recognize → Excise → Resynthesize → Ligate All three pathways share the "cut and patch" logic but differ in recognition and excision scope

Base Excision Repair (BER)

BER handles small, non-helix-distorting lesions: oxidized bases (e.g., 8-oxoguanine), deaminated bases (uracil in DNA), and alkylation products. These are chemically altered bases that do not significantly bend the double helix.

1
DNA glycosylase recognizes and cleaves the damaged base, creating an AP site (apurinic/apyrimidinic).
2
AP endonuclease nicks the sugar-phosphate backbone at the AP site.
3
DNA polymerase \(\beta\) fills the single-nucleotide gap using the intact strand as template.
4
DNA ligase III seals the remaining nick to restore continuity.

BER: Step-by-Step Diagram

1. Recognition X Glycosylase 2. Base removal AP site 3. Backbone nick / AP endonuclease 4. Gap fill C
Pol \(\beta\) + Ligase
 BER Scope: 1 nucleotide replaced Short-patch BER (most common) or long-patch BER (2-10 nt) Key Enzymes DNA Glycosylase OGG1, UDG, MPG APE1 AP endonuclease
Pol \(\beta\) / Ligase III
Gap fill + seal
 Clinical: OGG1 deficiency → increased 8-oxoG → oxidative mutagenesis

Nucleotide Excision Repair (NER)

NER targets bulky, helix-distorting lesions that BER cannot handle: UV-induced cyclobutane pyrimidine dimers (CPDs), 6-4 photoproducts, and large chemical adducts. NER removes a short oligonucleotide (24-32 nt in eukaryotes) flanking the damage.

1
Damage recognition: XPC-RAD23B senses helix distortion (global genome NER) or stalled RNA Pol II triggers repair (transcription-coupled NER).
2
Helix opening: TFIIH helicases (XPB, XPD) unwind ~30 bp around the lesion.
3
Dual incision: XPG cuts 3' and ERCC1-XPF cuts 5', releasing a 24-32 nt fragment.
4
Gap filling and ligation: DNA Pol \(\delta\)/\(\varepsilon\) resynthesizes; DNA ligase I seals.

NER: Dual Incision Model

Helix-distorting lesion (e.g., thymine dimer) T=T 5' cut ERCC1-XPF 3' cut XPG 24-32 nt excised After Excision + Resynthesis
New DNA synthesized by Pol \(\delta\)/\(\varepsilon\) + Ligase I
 GG-NER: XPC-RAD23B scans genome TC-NER: Stalled RNA Pol II triggers

Mismatch Repair (MMR)

MMR corrects replication errors that escape DNA polymerase proofreading: base-base mismatches and small insertion/deletion loops (IDLs). The critical challenge is identifying which strand carries the error: MMR targets the newly synthesized (daughter) strand.

1
Mismatch recognition: \(\text{MutS}\alpha\) (MSH2-MSH6) detects base mismatches; \(\text{MutS}\beta\) (MSH2-MSH3) detects IDLs.
2
Strand discrimination: \(\text{MutL}\alpha\) (MLH1-PMS2) identifies the daughter strand via nicks/gaps from replication. In E. coli, MutH cleaves hemimethylated GATC sites.
3
Excision: Exonuclease 1 (EXO1) degrades the error-containing daughter strand past the mismatch.
4
Resynthesis and ligation: DNA Pol \(\delta\) fills the gap; DNA ligase I seals.

MMR: Strand Discrimination

Parent strand (template) ...A-T-G-C-T-A-G... Daughter strand (newly synthesized) ...T-A-C-A-A-T-C... Mismatch! G:A instead of G:C
\(\text{MutS}\alpha\)
MSH2 + MSH6
\(\text{MutL}\alpha\)
MLH1 + PMS2
 EXO1 excises daughter strand
Pol \(\delta\) resynthesizes + Ligase I seals
 E. coli: MutH cleaves GATC

BER vs NER: Key Distinction

BER
Removes a single damaged base (not helix-distorting). Replaces 1 nucleotide (short-patch) or 2-10 nt (long-patch). Uses glycosylase for specificity.
NER
Removes a 24-32 nucleotide oligomer spanning a bulky, helix-distorting lesion. Uses dual endonuclease incisions. No glycosylase involved.

Two Sub-pathways of NER

GG-NER
Global Genome NER scans the entire genome for helix distortions. XPC-RAD23B is the sensor. Repairs lesions anywhere, but slower on non-transcribed DNA.
TC-NER
Transcription-Coupled NER is triggered when RNA Polymerase II stalls at a lesion. CSA and CSB proteins recruit NER machinery. Faster, but only repairs the transcribed strand.

How to Identify the Pathway

1
Identify the lesion type: Is the base chemically altered but small (oxidation, deamination, alkylation)? → BER
2
Does it distort the helix? UV dimer, bulky adduct, or cross-link? → NER
3
Is the base chemically normal but mispaired? Wrong base or small insertion/deletion from replication? → MMR
4
Check the excision scope: 1 nt = BER. 24-32 nt = NER. Variable (past mismatch) = MMR.
5
Key enzyme hint: Glycosylase? BER. XPC/TFIIH? NER. MSH2/MLH1? MMR.

Example 1: Oxidized Guanine

Reactive oxygen species convert guanine to 8-oxoguanine (8-oxoG). This altered base can mispair with adenine instead of cytosine during replication, causing G:C → T:A transversion mutations.

Example 2: UV-Induced Thymine Dimer

Ultraviolet light causes adjacent thymine bases to form covalent cyclobutane pyrimidine dimers (CPDs). The dimer kinks the DNA helix, blocking both replication and transcription.

Example 3: G-T Mismatch After Replication

During S phase, DNA Pol \(\delta\) occasionally incorporates thymine opposite guanine. The proofreading exonuclease misses it, leaving a G:T mismatch in the newly replicated DNA.

Common Mistakes

✕ Confusing BER and NER triggers
BER handles small, non-distorting base damage. NER handles bulky, helix-distorting lesions. The key is helix distortion, not damage severity.
✕ Thinking MMR fixes damaged bases
MMR fixes normal but mispaired bases. If a base is chemically altered (oxidized, deaminated), that is BER territory, even if it causes a mismatch.
✕ Forgetting strand discrimination in MMR
MMR must identify the daughter strand to avoid removing the correct template base. In E. coli, this uses methylation (Dam/GATC). In eukaryotes, it uses replication-associated nicks.

Summary Comparison

Feature BER NER MMR
Lesion Type Small base modification Bulky, helix-distorting Mispaired normal bases
Examples 8-oxoG, uracil, alkylation CPDs, 6-4PP, benzo[a]pyrene G:T, IDLs
Recognition DNA glycosylase XPC / stalled RNA Pol II \(\text{MutS}\alpha\) / \(\text{MutS}\beta\)
Excision Size 1 nt (short-patch) 24-32 nt Variable (past mismatch)
Key Polymerase Pol \(\beta\) Pol \(\delta\) / \(\varepsilon\) Pol \(\delta\)
Ligase Ligase III Ligase I Ligase I
Disease Link MUTYH polyposis Xeroderma Pigmentosum Lynch Syndrome (HNPCC)

Question 1 of 5

A cell is exposed to reactive oxygen species that convert guanine to 8-oxoguanine. Which repair pathway will primarily correct this lesion?

Question 2 of 5

In eukaryotic NER, approximately how many nucleotides are excised in the oligonucleotide fragment containing the lesion?

Question 3 of 5

A patient with Lynch Syndrome has a germline mutation in MLH1. Which DNA repair pathway is defective, and what molecular hallmark results?

Question 4 of 5

What is the critical difference between GG-NER and TC-NER?

Question 5 of 5

During mismatch repair, how does the eukaryotic MMR system distinguish the newly synthesized daughter strand from the parental template strand?