Targeting Base Excision Repair Glycosylases with DNA Containing Transition State Mimics Prepared via Click Chemistry

Philip K. Yuen, Sydnee A. Green, Jonathan Ashby, Kori T. Lay, Abhishek Santra, Xi Chen, Martin P. Horvath, Sheila S. David

Research output: Contribution to journalArticle

Abstract

DNA glycosylases of the base excision repair (BER) pathway are front-line defenders in removing compromising modifications of the DNA nucleobases. Aberrantly modified nucleobases mediate genomic mutations and inhibit DNA replication leading to adverse health consequences such as cancer, neurological diseases, and aging. In an effort to develop high-affinity transition state (TS) analogues as chemical biology probes for DNA glycosylases, oligonucleotides containing a propargyl-modified pyrrolidine TS mimic nucleotide were synthesized. A small library of TS mimic-containing oligonucleotides was generated using a structurally diverse set of five azides via copper(I)-catalyzed azide-alkyne cycloaddition "click" chemistry. The relative affinity (Kd) was evaluated for BER glycosylases Escherichia coli MutY, bacterial formamidopyrimidine glycosylase (Fpg), and human OG glycosylase 1 (hOGG1) with the library of TS mimic DNA duplexes. All of the BER glycosylases were found to exhibit extremely high affinities (approximately picomolar Kd values) for the TS mimics. However, binding preferences, distinct for each glycosylase, for the TS mimic library members were observed, suggesting different modes of binding and transition state stabilization among the three glycosylases. Fpg bound all of the TS mimics with exceptionally high affinities, while the MutY binding affinity correlated inversely with the size of the appended moiety. Of note, we identified one member of the small TS mimic library that exhibited a particularly high affinity for hOGG1. These results strongly support the use of the propargyl-TS mimic oligonucleotides and elaboration via click chemistry in screening and identification of high-affinity ligands for BER glycosylases of interest.

Original languageEnglish (US)
Pages (from-to)27-36
Number of pages10
JournalACS Chemical Biology
Volume14
Issue number1
DOIs
StatePublished - Jan 18 2019

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Click Chemistry
DNA Glycosylases
DNA Repair
Libraries
Repair
Oligonucleotides
Azides
DNA
Alkynes
Cycloaddition
Cycloaddition Reaction
DNA Replication
Escherichia coli
Copper
Screening
Nucleotides
Stabilization
Aging of materials
Health
Ligands

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine

Cite this

Targeting Base Excision Repair Glycosylases with DNA Containing Transition State Mimics Prepared via Click Chemistry. / Yuen, Philip K.; Green, Sydnee A.; Ashby, Jonathan; Lay, Kori T.; Santra, Abhishek; Chen, Xi; Horvath, Martin P.; David, Sheila S.

In: ACS Chemical Biology, Vol. 14, No. 1, 18.01.2019, p. 27-36.

Research output: Contribution to journalArticle

Yuen, Philip K. ; Green, Sydnee A. ; Ashby, Jonathan ; Lay, Kori T. ; Santra, Abhishek ; Chen, Xi ; Horvath, Martin P. ; David, Sheila S. / Targeting Base Excision Repair Glycosylases with DNA Containing Transition State Mimics Prepared via Click Chemistry. In: ACS Chemical Biology. 2019 ; Vol. 14, No. 1. pp. 27-36.
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