Single-molecule studies of repair proteins in base excision repair

BMB Rep. 2025 Jan;58(1):17-23. doi: 10.5483/BMBRep.2024-0178.

Abstract

Base excision repair (BER) is an essential cellular mechanism that repairs small, non-helix-distorting base lesions in DNA, resulting from oxidative damage, alkylation, deamination, or hydrolysis. This review highlights recent advances in understanding the molecular mechanisms of BER enzymes through single-molecule studies. We discuss the roles of DNA glycosylases in lesion recognition and excision, with a focus on facilitated diffusion mechanisms such as sliding and hopping that enable efficient genome scanning. The dynamics of apurinic/apyrimidinic endonucleases, especially the coordination between APE1 and DNA polymerase β (Pol β), are explored to demonstrate their crucial roles in processing abasic sites. The review further explores the short-patch and long-patch BER pathways, emphasizing the activities of Pol β, XRCC1, PARP1, FEN1, and PCNA in supporting repair synthesis and ligation. Additionally, we highlight the emerging role of UV-DDB as a general damage sensor in BER, extending its recognized function beyond nucleotide excision repair. Single-molecule techniques have been instrumental in uncovering the complex interactions and mechanisms of BER proteins, offering unprecedented insights that could guide future therapeutic strategies for maintaining genomic stability. [BMB Reports 2025; 58(1): 17-23].

Publication types

  • Review

MeSH terms

  • DNA / metabolism
  • DNA Damage
  • DNA Glycosylases / metabolism
  • DNA Polymerase beta* / metabolism
  • DNA Repair*
  • DNA-(Apurinic or Apyrimidinic Site) Lyase* / metabolism
  • Excision Repair
  • Flap Endonucleases / metabolism
  • Humans
  • Proliferating Cell Nuclear Antigen / metabolism
  • Single Molecule Imaging* / methods
  • X-ray Repair Cross Complementing Protein 1 / metabolism

Substances

  • DNA Polymerase beta
  • DNA-(Apurinic or Apyrimidinic Site) Lyase
  • X-ray Repair Cross Complementing Protein 1
  • DNA Glycosylases
  • APEX1 protein, human
  • Flap Endonucleases
  • DNA
  • Proliferating Cell Nuclear Antigen