Inhibition of uracil DNA glycosylase by an oxacarbenium ion mimic

Yu Lin Jiang, Yoshitaka Ichikawa, James Stivers

Research output: Contribution to journalArticle

Abstract

We have investigated the inhibition of the DNA repair enzyme uracil DNA glycosylase (UDG) by an 11-mer oligonucleotide (AIA) containing a cationic 1-aza-deoxyribose (I) residue designed to be a stable mimic of the high-energy oxacarbenium ion reaction intermediate [Werner, R. M., and Stivers, J. T. (2000) Biochemistry 39, 14054-14064]. Inhibition kinetics and direct binding studies indicate that AIA binds weakly to the free enzyme (KD = 2 μM) but binds 4000-fold more tightly to the enzymeuracil anion (EU) product complex (KD = 500 pM). The importance of the positive charge on the 1-nitrogen in binding is established by the observation that AIA binds - binary product complex is moderate (1 μM-1 s-1). Accordingly, the low KD of AIA for the EU complex is largely due its very slow off-rate (5 × 10-4 s-1). These results support previous kinetic isotope effect measurements that indicate UDG stabilizes a discrete oxacarbenium ion-uracil anion intermediate. This oxacarbenium ion mimic represents the tightest binding inhibitor of UDG yet identified.

Original languageEnglish (US)
Pages (from-to)7116-7124
Number of pages9
JournalBiochemistry®
Volume41
Issue number22
DOIs
StatePublished - Jun 4 2002

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Uracil-DNA Glycosidase
Anions
Ions
DNA Repair Enzymes
Deoxyribose
Reaction intermediates
Biochemistry
Kinetics
Uracil
Oligonucleotides
Isotopes
Nitrogen
Enzymes

ASJC Scopus subject areas

  • Biochemistry

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Inhibition of uracil DNA glycosylase by an oxacarbenium ion mimic. / Jiang, Yu Lin; Ichikawa, Yoshitaka; Stivers, James.

In: Biochemistry®, Vol. 41, No. 22, 04.06.2002, p. 7116-7124.

Research output: Contribution to journalArticle

Jiang, Yu Lin ; Ichikawa, Yoshitaka ; Stivers, James. / Inhibition of uracil DNA glycosylase by an oxacarbenium ion mimic. In: Biochemistry®. 2002 ; Vol. 41, No. 22. pp. 7116-7124.
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