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SNP-Associated Substitutions of Amino Acid Residues in the dNTP Selection Subdomain Decrease Polβ Polymerase

Olga A Kladova1, Timofey E Tyugashev1, Aleksandr A Miroshnikov2

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Summary

Single-nucleotide polymorphisms in the DNA polymerase β (Polβ) gene can alter its function. Variants G274R, G290C, and R333W show reduced activity, potentially increasing unrepaired DNA damage.

Keywords:
DNA polymerase betaDNA repairenzymatic activitysingle-nucleotide polymorphism

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • DNA polymerase β (Polβ) is crucial for genome stability and base excision repair (BER).
  • Single-nucleotide polymorphisms (SNPs) in the POLB gene can lead to altered Polβ enzymatic properties and are linked to cancer.
  • Specific amino acid positions (Gly-274, Gly-290, Arg-333) are implicated in Polβ function and have been observed in tumors.

Purpose of the Study:

  • To investigate the functional impact of naturally occurring polymorphic variants G274R, G290C, and R333W of DNA polymerase β.
  • To elucidate how these specific amino acid substitutions affect Polβ's enzymatic activity, DNA binding, and polymerization efficiency.

Main Methods:

  • Kinetic analyses were performed to quantify the enzymatic activity of the Polβ variants.
  • Molecular dynamics simulations were employed to examine the structural and dynamic changes induced by the amino acid substitutions.
  • Assays for gap-filling, primer elongation, and deoxynucleotide triphosphate binding were conducted.

Main Results:

  • All three polymorphic variants (G274R, G290C, R333W) exhibited reduced polymerase activity.
  • The G274R and R333W substitutions significantly impaired gap-filling and primer elongation capabilities.
  • These variants showed decreased deoxynucleotide triphosphate binding affinity and lower polymerization constants, linked to altered local protein structures.

Conclusions:

  • The studied Polβ variants (G274R, G290C, R333W) possess diminished enzymatic functions.
  • These functional deficits suggest a potential role in the accumulation of unrepaired DNA damage.
  • The findings highlight the importance of specific Polβ residues in maintaining genome integrity and their implications in disease.