Excision repair pathways that correct bulky DNA lesions such as thymine dimers typically include several ordered steps. Which of the following steps are part of the mechanism?

Introduction / Context:
Nucleotide excision repair removes bulky lesions that distort the DNA helix, including UV induced thymine dimers and certain chemical adducts. The process involves damage recognition, cutting the strand, removing the damaged patch, resynthesis, and sealing. Understanding each step clarifies how integrity is restored.

Given Data / Assumptions:

• Damage distorts the double helix and is recognized by surveillance proteins.
• Repair enzymes act sequentially to excise and replace the damaged segment.
• DNA ligase completes the repair by sealing nicks.

Concept / Approach:
Canonical excision repair includes: incision (endonucleases cut on one or both sides of the lesion), excision (the damaged oligonucleotide is removed), repair synthesis (polymerase fills the gap using the undamaged strand as template), and ligation (DNA ligase seals the final phosphodiester bond). Different organisms have variant protein complexes, but the step logic is conserved.

Step-by-Step Solution:
Identify incision as endonucleolytic cutting flanking the lesion. Recognize excision as removal of the cut fragment. Acknowledge ligation as the final sealing after gap filling synthesis. Therefore, all listed steps belong to excision repair.

Verification / Alternative check:
Biochemical reconstitution of excision repair shows distinct incision and excision activities, followed by DNA polymerase and ligase actions to complete repair.

Why Other Options Are Wrong:

• Listing a single step is incomplete; the pathway requires all components.

Common Pitfalls:
Overlooking the synthesis step mentally; while not listed among the options, it occurs between excision and ligation, but the question focuses on incision, excision, and ligation as core named steps.

Final Answer:
All of these