What is Dr. Zubair Khalid's research focus?

Dr. Zubair Khalid specializes in molecular virology, mRNA vaccine development, and computational biology, with a focus on avian pathogens like IBDV and Avian Reovirus.

Where is Dr. Zubair Khalid currently working?

Dr. Zubair Khalid is a Postdoctoral Research Associate at the University of Maryland (UMD), specifically within the Department of Animal and Avian Sciences.

Nucleotide Excision Repair: Mechanism and Significance

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-08-11

Introduction to Nucleotide Excision Repair

What is Nucleotide Excision Repair?

Nucleotide excision repair (NER) is a highly conserved DNA repair pathway that removes bulky, helix-distorting lesions from the genome. Unlike pathways that fix single damaged bases, NER excises a short oligonucleotide fragment—typically 24–32 nucleotides in length—containing the lesion, then fills the resulting gap using the undamaged complementary strand as a template. This repair mechanism operates on a remarkable range of substrates, from ultraviolet (UV) light-induced photoproducts to large chemical adducts, making it one of the most versatile repair systems in the cell.

The pathway is defined by its dual incision mechanism: two endonucleolytic cuts flank the lesion, one on the 5′ side and one on the 3′ side, creating a single-stranded gap that is subsequently filled by DNA polymerases. This distinguishes NER from Base Excision Repair, which removes a single damaged base via a glycosylase-initiated pathway. NER also differs from mismatch repair, which corrects errors introduced during replication rather than chemical damage to existing DNA.

NER operates in all domains of life, from bacteria to humans, though the protein machinery has diverged significantly. In Escherichia coli, the UvrABC system performs the repair with just three proteins. In eukaryotes, the pathway requires more than 30 polypeptides, reflecting the greater complexity of chromatin and the need for regulatory integration with transcription and the cell cycle.

Types of DNA Damage Repaired by NER

NER recognizes lesions that cause significant distortion of the DNA double helix. The most biologically relevant substrates include:

UV-induced photoproducts. Cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs) are the primary DNA lesions caused by ultraviolet radiation. CPDs form covalent bonds between adjacent pyrimidines on the same strand, introducing a kink of approximately 30 degrees in the helix. 6-4PPs cause even greater distortion, shifting the helix by about 44 degrees. Both are efficiently repaired by NER.

Bulky chemical adducts. Polycyclic aromatic hydrocarbons, such as benzo[a]pyrene found in cigarette smoke, form large covalent adducts with guanine bases. Chemotherapeutic agents like cisplatin produce intrastrand crosslinks between adjacent purines. These adducts distort the helix and are NER substrates.

Crosslinking agents. Psoralen plus UVA light generates interstrand crosslinks that require NER for the initial unhooking step, though complete repair of these lesions also involves homologous recombination.

Endogenous lesions. Certain reactive oxygen species and lipid peroxidation products can generate bulky adducts that are processed by NER, although this constitutes a minor fraction of its physiological workload.

The common thread among these substrates is helical distortion. NER does not recognize the chemical nature of the damage per se; rather, it detects the structural perturbation that the lesion imposes on the DNA duplex. This explains the remarkable substrate versatility of the pathway.

The Two Subpathways: Global Genomic and Transcription-Coupled NER

NER is divided into two subpathways that share the same core excision machinery but differ in how damage is initially recognized. This division reflects a fundamental biological logic: lesions that block transcription are more immediately toxic than those in silent chromatin, so the cell prioritizes repair of the transcribed strand of active genes.

Global Genomic NER (GG-NER)

Global genomic NER operates throughout the genome, repairing lesions in both transcribed and non-transcribed regions, including those in chromatin. In mammalian cells, the initial damage recognition step is performed by the XPC–RAD23B complex, aided by the UV-damaged DNA-binding protein (UV-DDB) for certain lesions.

XPC–RAD23B recognizes the single-stranded character of DNA opposite the lesion, rather than the lesion itself. This is a crucial mechanistic point: XPC binds to the small region of unpaired bases that exist opposite a bulky adduct, effectively sensing the thermodynamic destabilization caused by the damage. The complex has a high affinity for the undamaged strand across from the lesion, which explains how it can recognize such chemically diverse substrates.

UV-DDB, composed of DDB1 and DDB2 (the product of the XPE gene), enhances recognition of CPDs, which are less helix-distorting than 6-4PPs and therefore more challenging for XPC to detect. UV-DDB binds the lesion directly, then recruits XPC–RAD23B to the site. Mutations in DDB2 cause a mild form of xeroderma pigmentosum (XP group E), underscoring the importance of this accessory factor.

Transcription-Coupled NER (TC-NER)

Transcription-coupled NER is initiated when RNA polymerase II (RNAPII) stalls at a lesion on the transcribed strand of an active gene. The stalled polymerase itself serves as the damage sensor, but it must be displaced or remodeled to allow repair proteins access to the lesion.

The key factor in TC-NER is the protein CSA (encoded by ERCC8) and CSB (encoded by ERCC6). CSB is a DNA-dependent ATPase that binds to the stalled RNAPII and recruits CSA, which is a component of a ubiquitin ligase complex (DDB1-CUL4-RBX1). This complex ubiquitinates RNAPII, leading to its ubiquitination and either removal or remodeling, depending on the severity of the damage. For repairable lesions, RNAPII is transiently backtracked to expose the lesion; for irreparable damage, the polymerase is polyubiquitinated and degraded.

TC-NER does not require XPC–RAD23B, since the stalled polymerase provides the recognition signal. However, all downstream factors—TFIIH, XPA, RPA, XPG, and XPF-ERCC1—are shared between the two subpathways. This explains why mutations in the core excision factors cause XP, while mutations in CSA or CSB cause Cockayne syndrome, a distinct clinical entity.

The biological significance of TC-NER is profound: it ensures that the most important genes—those actively transcribed—are preferentially repaired. This prioritization is essential because a single unrepaired lesion in an essential gene can block transcription and trigger apoptosis.

Step-by-Step Mechanism of Nucleotide Excision Repair

The NER reaction can be divided into five sequential stages: damage recognition, unwinding and verification, dual incision, excision, and repair synthesis. The following describes the mechanism in human cells, which is the best-characterized eukaryotic system.

Damage Recognition

For GG-NER, the process begins with XPC–RAD23B binding to the site of helical distortion. XPC contains a β-hairpin domain that inserts into the DNA duplex at the lesion site, flipping out two nucleotides on the undamaged strand. This binding is stabilized by interactions with the single-stranded DNA that becomes exposed. RAD23B protects XPC from proteasomal degradation and stabilizes the complex.

For CPDs, UV-DDB binds first, recognizing the lesion directly through a pocket in DDB2. UV-DDB then recruits XPC–RAD23B, and the complex undergoes a conformational change that transfers the lesion from DDB2 to XPC. This handoff is essential because XPC alone binds CPDs poorly.

In TC-NER, the stalled RNAPII serves as the recognition platform. CSB is recruited to the stalled polymerase, followed by CSA and the ubiquitin ligase complex. The ubiquitination of RNAPII triggers a conformational change that exposes the lesion, allowing downstream NER factors to access the site.

Unwinding and Verification

Once XPC–RAD23B (or the stalled polymerase in TC-NER) is positioned at the lesion, the transcription factor TFIIH is recruited. TFIIH is a multi-subunit complex containing two helicases: XPB and XPD. XPB has 3′→5′ helicase activity and is responsible for initial promoter opening during transcription; in NER, it facilitates the unwinding of the DNA duplex around the lesion. XPD has 5′→3′ helicase activity and translocates along the damaged strand, acting as a molecular ruler that verifies the presence of damage.

The helicase activities of XPB and XPD require ATP hydrolysis. XPD translocates along the DNA in the 5′→3′ direction, and its progress is blocked by the lesion. This blockage serves as a verification step: if XPD can pass, the DNA is not damaged, and the repair complex disassembles. If XPD stalls, the lesion is confirmed, and the complex proceeds to the next step. This proofreading mechanism prevents futile repair at undamaged sites.

The unwinding reaction opens the DNA duplex over approximately 20–30 base pairs, creating a bubble structure. This open complex is stabilized by the single-stranded DNA-binding protein RPA, which coats the undamaged strand. XPA is also recruited at this stage; it binds to the junction between double-stranded and single-stranded DNA at the 5′ side of the lesion and helps position the endonucleases.

Dual Incision and Excision

The dual incision step is performed by two structure-specific endonucleases. XPG cleaves the damaged strand on the 3′ side of the lesion, while the XPF-ERCC1 heterodimer cleaves on the 5′ side. The incisions are not made at fixed distances from the lesion; rather, they are determined by the boundaries of the open complex.

XPG is recruited to the complex early, during the unwinding step, but its endonuclease activity is not activated until the full open complex is formed. XPG cleaves the damaged strand 2–8 nucleotides from the 3′ side of the lesion. XPF-ERCC1 is recruited later, after XPA and RPA are in place, and cleaves 15–24 nucleotides from the 5′ side of the lesion.

The dual incision releases a single-stranded oligonucleotide of 24–32 nucleotides containing the lesion. This fragment is then displaced from the duplex, leaving a single-stranded gap that is coated by RPA. The gap is bounded by a 3′-hydroxyl group at the 5′ incision site and a 5′-phosphate at the 3′ incision site.

Repair Synthesis and Ligation

The gap is filled by a DNA polymerase, primarily DNA polymerase δ or ε, in conjunction with the processivity factor PCNA and the clamp loader RFC. The replication factor C (RFC) loads PCNA onto the DNA at the 3′ hydroxyl group, and the polymerase extends the primer, copying the undamaged template strand.

The repair synthesis step is coupled to the excision step: as the polymerase synthesizes new DNA, it displaces RPA from the template. The final nick is sealed by DNA ligase I or ligase IIIα. DNA ligase I is the primary ligase for NER in replicating cells, while ligase IIIα (in complex with XRCC1) may function in non-dividing cells.

The entire process—from damage recognition to ligation—takes approximately 30–60 minutes in human cells, with the incision and synthesis steps being the fastest. The rate-limiting step is damage recognition, particularly for CPDs in chromatin.

Key Proteins and Their Functions in NER

Core NER Factors

The core NER machinery in humans consists of approximately 10 proteins, many of which are named for their association with xeroderma pigmentosum (XP) complementation groups. The following table summarizes their functions:

Protein	Gene	Function in NER
XPC	XPC	Damage recognition in GG-NER; binds helix distortion
RAD23B	RAD23B	Stabilizes XPC; protects from degradation
UV-DDB	DDB1/DDB2	Enhances recognition of CPDs; recruits XPC
XPB	ERCC3	3′→5′ helicase; ATP-dependent unwinding
XPD	ERCC2	5′→3′ helicase; damage verification
XPA	XPA	Scaffold; verifies damage; positions endonucleases
RPA	RPA1-3	Binds single-stranded DNA; stabilizes open complex
XPG	ERCC5	3′ endonuclease; makes 3′ incision
XPF	ERCC4	5′ endonuclease; makes 5′ incision
ERCC1	ERCC1	Forms heterodimer with XPF; required for stability
CSA	ERCC8	TC-NER; ubiquitin ligase component
CSB	ERCC6	TC-NER; ATPase; binds stalled RNAPII

The XPF-ERCC1 heterodimer is particularly interesting: ERCC1 has no catalytic activity but is required for the stability and proper folding of XPF. The complex cleaves at the junction between double-stranded and single-stranded DNA, with a preference for a 5′ overhang. This structure-specific activity ensures that the incision is made at the correct position relative to the lesion.

The Role of TFIIH in NER

TFIIH is a remarkable complex that serves dual functions in transcription and NER. It consists of 10 subunits: XPB, XPD, p62, p52, p44, p34, and the CDK-activating kinase (CAK) subcomplex containing CDK7, cyclin H, and MAT1.

In transcription, TFIIH is required for promoter melting during initiation by RNA polymerase II. In NER, the same complex is recruited to the lesion site, but its function is different: the helicase activities of XPB and XPD are used to unwind the DNA around the lesion, creating the open complex.

The CAK subcomplex, which phosphorylates the C-terminal domain of RNAPII during transcription, is dispensable for NER in vitro. However, its presence in the complex may have regulatory functions in vivo. Mutations in the CAK subunits are associated with trichothiodystrophy, a disorder characterized by brittle hair and developmental defects, rather than the cancer predisposition seen in XP.

The dual role of TFIIH explains why mutations in XPB and XPD can cause either XP, trichothiodystrophy, or combined phenotypes, depending on which function is affected. This genotype-phenotype correlation is a fascinating example of how a single protein complex can serve distinct cellular processes.

How Nucleotide Excision Repair Is Studied

In Vitro Repair Assays

The development of cell-free NER assays in the 1980s was a landmark achievement that enabled the biochemical dissection of the pathway. The standard assay uses a plasmid DNA substrate containing a defined lesion, typically a single CPD or 6-4PP, incubated with whole-cell extracts from cultured human cells.

The reaction mixture typically contains:

100–200 ng of damaged plasmid DNA
50–100 μg of whole-cell extract protein
2 mM ATP
40 mM creatine phosphate and 2 μg creatine phosphokinase (ATP regenerating system)
50 μM each of dATP, dGTP, dTTP, and [α-32P]dCTP
40 mM HEPES-KOH (pH 7.8)
5 mM MgCl₂
0.5 mM DTT

The reaction is incubated at 30°C for 1–2 hours. Repair synthesis is detected by autoradiography after agarose gel electrophoresis, which separates the closed-circular plasmid from the nicked form. The incorporation of radiolabeled nucleotides into the repaired plasmid is quantified by phosphorimaging.

A complementary approach is the dual incision assay, which uses a linear DNA substrate with a lesion at a defined position. After incubation with extract, the excised oligonucleotide is detected by denaturing polyacrylamide gel electrophoresis. This assay directly measures the incision step and can be used to determine the exact positions of the 5′ and 3′ cuts.

Cell-Based Repair Assays

Cell-based assays measure NER activity in living cells. The most widely used is the host cell reactivation assay, in which a reporter plasmid (e.g., expressing firefly luciferase) is damaged with UV light and transfected into cells. The level of reporter gene expression reflects the capacity of the cells to repair the damaged plasmid. Cells with NER defects show reduced reactivation compared to wild-type cells.

Another approach is the unscheduled DNA synthesis (UDS) assay, which measures repair synthesis in non-replicating cells. Cells are treated with UV light, then incubated with [3H]thymidine or bromodeoxyuridine (BrdU). Incorporation of the label into DNA outside of S phase indicates active repair synthesis. UDS is detected by autoradiography or immunofluorescence with anti-BrdU antibodies.

More recently, the comet assay (single-cell gel electrophoresis) has been adapted to measure NER. Cells are damaged with UV, allowed to repair for varying times, then embedded in agarose and subjected to electrophoresis under alkaline conditions. The extent of DNA migration (the "comet tail") reflects the amount of DNA damage present. As repair proceeds, the tail length decreases.

Genetic and Molecular Approaches

The genetic dissection of NER has been instrumental in identifying the components of the pathway. The isolation of UV-sensitive mutants in yeast (Saccharomyces cerevisiae and Schizosaccharomyces pombe) led to the identification of the RAD genes, many of which are conserved in humans. Complementation analysis of cells from XP patients defined the seven complementation groups (XP-A through XP-G) that correspond to mutations in different NER genes.

Modern approaches include:

CRISPR-Cas9 gene editing. This technology allows the generation of isogenic cell lines with specific mutations in NER genes, enabling the study of genotype-phenotype relationships in a controlled genetic background.

Chromatin immunoprecipitation (ChIP). ChIP with antibodies against NER proteins can map the recruitment of repair factors to damaged regions of the genome. Sequential ChIP (ChIP-reChIP) can establish the order of factor recruitment.

Single-molecule imaging. Fluorescence microscopy techniques, including single-molecule tracking, can visualize the dynamics of NER protein binding and dissociation in living cells. These studies have revealed that XPC undergoes rapid, transient binding to undamaged DNA and longer-lived binding at lesion sites.

Genomic approaches. The development of excision repair sequencing (XR-seq) has enabled genome-wide mapping of NER activity. This technique captures the excised oligonucleotide fragments and sequences them, providing a high-resolution view of where and how efficiently NER operates across the genome.

Clinical Relevance: Diseases Associated with NER Defects

Mutations in NER genes cause a spectrum of human diseases with distinct clinical features. The three major disorders are xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy, each resulting from mutations in specific components of the pathway.

Xeroderma Pigmentosum (XP)

Xeroderma pigmentosum is an autosomal recessive disorder characterized by extreme sensitivity to sunlight, a >1000-fold increased risk of skin cancer, and progressive neurological degeneration in about 20% of patients. The disease is caused by mutations in any of seven genes (XPA through XPG) or in DDB2 (XP-E).

The hallmark of XP is the failure to repair UV-induced photoproducts, leading to the accumulation of mutations in sunlight-exposed skin. Patients develop freckling, skin atrophy, and multiple skin cancers (basal cell carcinoma, squamous cell carcinoma, melanoma) at an early age—often in the first decade of life. The median age of first skin cancer in XP patients is approximately 8 years, compared to 60 years in the general population.

The neurological features of XP are more variable and correlate with the specific gene mutated. XP-A, XP-B, XP-D, and XP-G patients often have severe neurological symptoms, including microcephaly, intellectual disability, and sensorineural hearing loss. These symptoms are thought to result from the accumulation of oxidative DNA damage in neurons, which are post-mitotic and cannot dilute damage through replication. XP-C and XP-E patients typically have minimal or no neurological involvement, consistent with the fact that these proteins are only required for GG-NER, not TC-NER.

Cockayne Syndrome (CS)

Cockayne syndrome is caused by mutations in ERCC8 (CSA) or ERCC6 (CSB), the two genes specific to TC-NER. Unlike XP, CS is not associated with increased skin cancer risk. Instead, the disease is characterized by severe growth failure, progressive neurological dysfunction, retinal degeneration, and characteristic facial features (deep-set eyes, prominent ears, and a beaked nose).

The clinical features of CS reflect the importance of TC-NER for the repair of transcription-blocking lesions. Without functional CSA or CSB, cells cannot repair damage on the transcribed strand of active genes, leading to prolonged transcription arrest and apoptosis. The progressive neurodegeneration in CS is thought to result from the accumulation of unrepaired oxidative lesions in post-mitotic neurons.

CS patients also show features of premature aging, including loss of subcutaneous fat, hearing loss, and cataracts. The average lifespan is approximately 12 years, with death typically resulting from respiratory failure or complications of neurodegeneration.

Trichothiodystrophy (TTD)

Trichothiodystrophy is a rare disorder caused by mutations in XPB, XPD, or TTDN1 (a gene of unknown function). The hallmark feature is brittle, sulfur-deficient hair caused by reduced levels of cysteine-rich matrix proteins. Patients also show ichthyosis (scaly skin), intellectual disability, and increased susceptibility to infections.

TTD is unique among NER disorders because it is not associated with increased skin cancer risk, despite the fact that cells from TTD patients show reduced NER activity. This paradox is explained by the fact that the mutations in XPB and XPD that cause TTD specifically affect the transcriptional function of TFIIH, not its repair function. The hair and skin abnormalities are thought to result from reduced expression of specific genes during development, rather than from DNA repair defects.

The distinction between XP and TTD illustrates an important principle: mutations in the same gene can cause different diseases depending on which function of the protein is affected. XPD mutations that impair helicase activity cause XP, while mutations that affect the stability or assembly of TFIIH cause TTD.

Common Pitfalls and Misconceptions in NER

NER vs. Base Excision Repair

A frequent source of confusion is the distinction between NER and Base Excision Repair. Both pathways handle DNA damage, but they differ fundamentally in their substrates and mechanisms.

Base excision repair (BER) handles small, non-helix-distorting lesions such as oxidized bases (8-oxoguanine), alkylated bases (3-methyladenine), and uracil. The pathway is initiated by a DNA glycosylase that cleaves the N-glycosidic bond, releasing the damaged base and creating an abasic (AP) site. An AP endonuclease then nicks the backbone, and the gap is filled by a polymerase and sealed by a ligase. BER typically replaces a single nucleotide (short-patch BER) or 2–13 nucleotides (long-patch BER).

NER, in contrast, handles bulky, helix-distorting lesions and always removes a 24–32 nucleotide fragment. NER does not use glycosylases; instead, it uses structure-specific endonucleases that recognize the distortion. The key distinction is the size of the lesion and the degree of helical distortion: small, non-distorting lesions go to BER; large, distorting lesions go to NER.

A useful mnemonic: BER = "base" excision, removing just the base; NER = "nucleotide" excision, removing a patch of nucleotides.

Misunderstanding the Incision Step

Students often assume that the dual incisions are made at fixed distances from the lesion. In reality, the incision sites are determined by the boundaries of the open complex, which can vary depending on the lesion and the specific proteins involved. The 3′ incision by XPG is typically 2–8 nucleotides from the lesion, while the 5′ incision by XPF-ERCC1 is 15–24 nucleotides away. The excised fragment is therefore 24–32 nucleotides long, but the exact length varies.

Another common error is the assumption that XPG makes the 5′ incision and XPF-ERCC1 makes the 3′ incision. This is incorrect: XPG cleaves on the 3′ side of the lesion, and XPF-ERCC1 cleaves on the 5′ side. The nomenclature refers to the position relative to the lesion, not the direction of the incision.

Overlooking Transcription-Coupled Repair

Many students learn NER as a single pathway and overlook the distinction between GG-NER and TC-NER. This is a critical omission, as the two subpathways have different recognition mechanisms, different protein requirements, and different clinical consequences.

GG-NER requires XPC-RAD23B and UV-DDB for damage recognition. TC-NER does not require these factors; instead, it uses the stalled RNAPII as the damage sensor, with CSB and CSA as the key recognition factors. Mutations in XPC cause XP but not CS, while mutations in CSA or CSB cause CS but not XP. Understanding this distinction is essential for interpreting the clinical phenotypes of NER disorders.

A related misconception is that TC-NER only repairs the transcribed strand. In fact, TC-NER repairs lesions on the transcribed strand of active genes, while GG-NER repairs both strands throughout the genome. The transcribed strand of active genes is repaired faster than the non-transcribed strand because TC-NER is more efficient than GG-NER.

Summary and Exam Tips

Quick Recap of NER Steps

Damage recognition: XPC-RAD23B (GG-NER) or stalled RNAPII (TC-NER) detects the helix distortion.
Unwinding and verification: TFIIH (XPB and XPD helicases) unwinds the DNA; XPD verifies the lesion.
Dual incision: XPG cleaves 3′ to the lesion; XPF-ERCC1 cleaves 5′ to the lesion.
Excision: The 24–32 nucleotide fragment containing the lesion is released.
Repair synthesis: DNA polymerase δ/ε fills the gap using the undamaged strand as template.
Ligation: DNA ligase I seals the nick.

Mnemonics and Memory Aids

The order of incision: "XPG is on the 3′ side, XPF-ERCC1 is on the 5′ side." Remember: "G" comes before "F" in the alphabet, and 3′ comes before 5′ when reading DNA in the 5′→3′ direction. So XPG (G) makes the 3′ incision, and XPF (F) makes the 5′ incision.

The XP complementation groups: "A, B, C, D, E, F, G" correspond to the proteins XPA, XPB, XPC, XPD, XPE (DDB2), XPF, and XPG. A useful mnemonic: "All Bright Children Do Excellent Fine Genetics."

NER vs. BER: "NER removes a patch, BER removes a patch." More precisely: NER removes 24–32 nucleotides; BER removes 1–13 nucleotides. "NER is for big damage, BER is for small damage."

TC-NER factors: "CSA and CSB are for Cockayne Syndrome." The "C" in CSA/CSB and Cockayne helps link them.

TFIIH subunits: "XPB unwinds, XPD verifies." XPB has 3′→5′ helicase activity; XPD has 5′→3′ helicase activity. XPD translocates along the damaged strand and stalls at the lesion, providing the verification step.

Frequently Asked Questions

What is nucleotide excision repair?

Nucleotide excision repair (NER) is a DNA repair pathway that removes bulky, helix-distorting lesions from the genome. It excises a short oligonucleotide fragment (24–32 nucleotides) containing the damage, then fills the gap using the undamaged complementary strand as a template. NER is the primary mechanism for repairing UV-induced photoproducts and large chemical adducts.

What are the steps of nucleotide excision repair?

The steps are: (1) damage recognition by XPC-RAD23B (GG-NER) or stalled RNAPII (TC-NER); (2) unwinding of the DNA duplex by TFIIH helicases XPB and XPD; (3) dual incision by XPG (3′ side) and XPF-ERCC1 (5′ side); (4) excision of the 24–32 nucleotide fragment; (5) repair synthesis by DNA polymerase δ/ε with PCNA; and (6) ligation by DNA ligase I.

What are the types of nucleotide excision repair?

There are two subpathways: global genomic NER (GG-NER), which operates throughout the genome and uses XPC-RAD23B for damage recognition, and transcription-coupled NER (TC-NER), which repairs lesions on the transcribed strand of active genes and uses stalled RNA polymerase II as the damage sensor.

How does nucleotide excision repair work?

NER works by detecting helical distortion caused by bulky lesions, unwinding the DNA around the lesion, making dual incisions on the damaged strand, excising the lesion-containing oligonucleotide, and filling the resulting gap by DNA synthesis. The process requires approximately 30 proteins in humans and takes 30–60 minutes per lesion.

What are examples of nucleotide excision repair?

Examples of NER substrates include cyclobutane pyrimidine dimers and 6-4 photoproducts caused by UV light, cisplatin-induced intrastrand crosslinks, benzo[a]pyrene-guanine adducts from cigarette smoke, and psoralen crosslinks. NER also repairs certain endogenous lesions such as those caused by reactive oxygen species.

What is the difference between nucleotide excision repair and base excision repair?

NER removes bulky, helix-distorting lesions as 24–32 nucleotide fragments using structure-specific endonucleases. Base Excision Repair removes small, non-distorting lesions (oxidized, alkylated, or deaminated bases) as single nucleotides or short patches using DNA glycosylases. NER recognizes helical distortion; BER recognizes specific damaged bases.

What proteins are involved in nucleotide excision repair?

The core NER proteins are XPC, RAD23B, UV-DDB (DDB1/DDB2), TFIIH (XPB, XPD, and associated subunits), XPA, RPA, XPG, XPF-ERCC1, PCNA, RFC, DNA polymerase δ/ε, and DNA ligase I. TC-NER additionally requires CSA and CSB.

Key Takeaways

NER removes bulky, helix-distorting DNA lesions by excising a 24–32 nucleotide fragment and resynthesizing the gap.
The pathway has two subpathways: GG-NER (genome-wide, XPC-dependent) and TC-NER (transcribed strand, CSB/CSA-dependent).
The dual incision is made by XPG (3′ side) and XPF-ERCC1 (5′ side), with the excised fragment length determined by the open complex boundaries.
TFIIH plays a dual role in transcription and NER, explaining the complex phenotypes of mutations in XPB and XPD.
NER defects cause xeroderma pigmentosum (cancer predisposition), Cockayne syndrome (neurodegeneration, no cancer), and trichothiodystrophy (developmental defects).
NER differs from BER in substrate specificity, mechanism, and the size of the excised fragment.
Understanding the distinction between GG-NER and TC-NER is essential for interpreting the clinical features of NER disorders.