Questions: Nucleotide Excision Repair (NER) and UV Lesions

Question 1

A newly discovered chemical creates a bulky covalent adduct on guanine that severely distorts the DNA double helix but does not chemically alter guanine's base-pairing properties. Which repair pathway is most likely responsible for removing this lesion?

• A. Base excision repair (BER) — because it targets chemically modified bases on guanine
• B. Mismatch repair (MMR) — because the adduct may cause mispairing during subsequent replication
• C. Nucleotide excision repair (NER) — because it recognizes helix-distorting structural disruption, not specific chemical identity
• D. Direct repair by photolyase — because photolyase reverses any covalent modification to nucleotide bases

Answer: (C)

NER is specifically suited to bulky, helix-distorting lesions because its damage recognition complex (XPC-RAD23B) detects structural disruption of the double helix — not any particular chemical modification. BER handles small, subtle lesions (oxidized, deaminated, or alkylated bases) that do not significantly distort the helix. The defining feature of NER substrates is their physical disruption of normal helix geometry, which is why NER handles a diverse range of chemically distinct lesions as long as they are bulky enough to warp the helix.

Question 2

A mutation in the XPG gene completely abolishes its endonuclease activity. What is the predicted consequence for NER?

• A. Damage recognition fails — XPG is required to detect helix distortions
• B. The NER bubble cannot form — XPG provides the helicase activity that unwinds DNA around the lesion
• C. The 3' incision on the damaged strand cannot be made, blocking excision of the damage-containing fragment
• D. Gap resynthesis fails — XPG is the polymerase that fills in the excised region

Answer: (C)

XPG is one of two endonucleases that make the dual incisions flanking the lesion: XPG cuts on the 3' side and XPF-ERCC1 cuts on the 5' side. Without the 3' cut, the ~25-29 nucleotide fragment containing the lesion cannot be released even if damage recognition, TFIIH helicase unwinding, and 5' incision all proceed normally. NER stalls at the excision step. This is why XPG mutations cause xeroderma pigmentosum — the damage is recognized and the repair machinery assembles, but the lesion is never removed.

Question 3

Nucleotide excision repair removes primarily the single damaged nucleotide and replaces it one base at a time, similar to base excision repair.

• T. True
• F. False

Answer: False

This is the key mechanistic distinction between NER and BER. BER does remove a single modified base (via a glycosylase) and then fills in one position. NER works by a fundamentally different 'cut and patch' strategy: dual endonuclease incisions on both sides of the lesion release an entire ~25-29 nucleotide single-stranded fragment containing the damage. This larger excision window is necessary because bulky, helix-distorting lesions disrupt multiple base pairs and cannot be addressed by single-nucleotide replacement.

Question 4

Transcription-coupled NER (TC-NER) is triggered when RNA polymerase II stalls at a DNA lesion, ensuring that actively expressed genes are repaired preferentially and faster than silent genomic regions.

• T. True
• F. False

Answer: True

TC-NER is activated when elongating RNA Pol II encounters and stalls at a NER-type lesion in the template strand. The stalled polymerase recruits CSA and CSB proteins, which bring in the core NER machinery. This creates a biological priority system: damage in actively transcribed genes — where it immediately blocks RNA synthesis — is repaired faster than equivalent damage in silenced regions. The clinical importance of this sub-pathway is illustrated by Cockayne syndrome: defects in TC-NER (CSA or CSB) cause developmental abnormalities and neurodegeneration despite intact global genome NER, showing the sub-pathways have distinct biological roles.

Question 5

What is the key structural feature that NER recognizes, and why does this allow it to repair a wider variety of lesions than base excision repair?

Model answer: NER recognizes helix distortion — the physical disruption of normal double-helix geometry — rather than any specific chemical modification. The XPC-RAD23B damage recognition complex detects the abnormal local structure created when a bulky lesion bends, unwinds, or destabilizes the helix, not the chemistry of the lesion itself. This structure-based recognition is what gives NER its broad substrate range: any lesion large enough to meaningfully distort the helix — UV photoproducts (CPDs and 6-4 photoproducts), bulky chemical adducts, some interstrand crosslinks — can be recognized and removed. BER, by contrast, uses specific glycosylases that each recognize a narrow set of chemical modifications, giving high specificity but limited scope.

This structural vs. chemical recognition logic illustrates a general principle in DNA repair: different pathways evolved to detect different classes of damage using fundamentally different sensor mechanisms. NER trades chemical specificity for breadth by reading the helix as a physical object; BER reads the chemistry directly. Neither approach alone covers all forms of DNA damage — which is why cells maintain multiple parallel repair pathways.