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Zinc-Binding Oligonucleotide Backbone Modifications for Targeting a DNA-Processing Metalloenzyme.

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  • 1National Institute for Bioprocess Research and Training, Foster Avenue, Mount Merrion, Dublin, Ireland.

Chembiochem : a European Journal of Chemical Biology
|July 18, 2024
PubMed
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This summary is machine-generated.

Chemically modified oligonucleotides were synthesized to inhibit the DNA repair enzyme SNM1A. A sulfinylacetamide-linked oligonucleotide showed potent inhibition, paving the way for DNA repair research tools.

Area of Science:

  • Medicinal Chemistry
  • Molecular Biology
  • Biochemistry

Background:

  • The DNA repair nuclease SNM1A plays a crucial role in maintaining genomic stability.
  • Targeting SNM1A is a potential strategy for cancer therapy and understanding DNA repair mechanisms.
  • Existing inhibitors often lack specificity or potency.

Purpose of the Study:

  • To design and synthesize novel chemically-modified oligonucleotides capable of inhibiting SNM1A.
  • To investigate the interaction of these modified oligonucleotides with the SNM1A active site.
  • To develop potential tools for studying DNA repair in vivo.

Main Methods:

  • Synthesis of dinucleoside phosphoramidites with modified internucleotide linkages (urea, squaramide, sulfanylacetamide, sulfinylacetamide).
Keywords:
DNA damageOligonucleotidesSNM1ASolid-phase oligonucleotide synthesisZinc-binding groups

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  • Solid-phase synthesis of modified oligonucleotides.
  • Gel electrophoresis-based assays to assess SNM1A interaction.
  • Real-time fluorescence assays to determine IC50 values.

    • Main Results:

    • Successfully synthesized and incorporated modified oligonucleotides into DNA strands.
    • Demonstrated interaction of all modified oligonucleotides with SNM1A, indicating enzyme inhibition.
    • Identified a sulfinylacetamide-linked oligonucleotide with the strongest SNM1A interaction.
    • Determined an IC50 value of 231 nM for the lead compound, significantly lower than previous inhibitors.

    Conclusions:

    • Novel chemically-modified oligonucleotides effectively inhibit the DNA repair enzyme SNM1A.
    • The sulfinylacetamide linkage shows particular promise for potent SNM1A inhibition.
    • These modified oligonucleotides represent a valuable scaffold for developing diagnostic and research probes for DNA repair studies.