Catalysts of DNA Strand Cleavage at Apurinic/Apyrimidinic Sites.

Irina G Minko,Thomas M Harris,Arnie R De Leon,Francesca Gruppi,R Stephen Lloyd,Amanda K Mccullough,Aaron C Jacobs,Nathan Donley,Carmelo J Rizzo

doi:10.1038/srep28894

Abstract

Apurinic/apyrimidinic (AP) sites are constantly formed in cellular DNA due to instability of the glycosidic bond, particularly at purines and various oxidized, alkylated, or otherwise damaged nucleobases. AP sites are also generated by DNA glycosylases that initiate DNA base excision repair. These lesions represent a significant block to DNA replication and are extremely mutagenic. Some DNA glycosylases possess AP lyase activities that nick the DNA strand at the deoxyribose moiety via a β- or β,δ-elimination reaction. Various amines can incise AP sites via a similar mechanism, but this non-enzymatic cleavage typically requires high reagent concentrations. Herein, we describe a new class of small molecules that function at low micromolar concentrations as both β- and β,δ-elimination catalysts at AP sites. Structure-activity relationships have established several characteristics that appear to be necessary for the formation of an iminium ion intermediate that self-catalyzes the elimination at the deoxyribose ring.

Highlights

Many DNA glycosylases, including human NEIL1, NEIL2, NEIL3, NTH1 and OGG1, possess AP lyase activities that catalyze either a β-or β,δ-elimination reaction at the deoxyribose moiety[9,11,12,13,14]
The initial observation that suggested the presence of an unusual activity in a subset of the small molecules under study was made when C1 (Fig. 1a) was tested as a potential inhibitor of hOGG1
While the position of the slower migrating product band corresponded to the β-elimination product of hOGG1 (Fig. 1d), the faster migrating product band co-migrated with the known δ-elimination product of hNEIL1 (Fig. 1e)

Summary

Introduction

Many DNA glycosylases, including human NEIL1, NEIL2, NEIL3, NTH1 and OGG1, possess AP lyase activities that catalyze either a β-or β,δ-elimination reaction at the deoxyribose moiety[9,11,12,13,14] This reaction proceeds via the formation of a transient enzyme-DNA covalent intermediate and generates DNA breaks with a phospho-α, β-unsaturated aldehyde or phosphate group at the 3′-end. In addition to these enzyme-catalyzed reactions, non-enzymatic cleavage of DNA at AP sites occurs under alkaline conditions or elevated temperatures[1,15,16] and in the presence of polyamines[9,15,17,18,19], histones[9,20], various nucleophilic peptides[21,22,23], or photoactivated metalloinserters[24]. We describe structure-activity and mechanistic studies of this new class of small molecule catalysts for DNA strand incision

Methods

Results

Conclusion