Insights into the Structures of DNA Damaged by Hydroxyl Radical: Crystal Structures of DNA Duplexes Containing 5-Formyluracil

Masaru Tsunoda,Takeshi Sakaue,Satoko Naito,Akira Matsuda,Akio Takénaka,Naoko Abe,Yoshihito Ueno,Tomoko Sunami

doi:10.4061/2010/107289

Abstract

Hydroxyl radicals are potent mutagens that attack DNA to form various base and ribose derivatives. One of the major damaged thymine derivatives is 5-formyluracil (fU), which induces pyrimidine transition during replication. In order to establish the structural basis for such mutagenesis, the crystal structures of two kinds of DNA d(CGCGRATfUCGCG) with R = A/G have been determined by X-ray crystallography. The fU residues form a Watson-Crick-type pair with A and two types of pairs (wobble and reversed wobble) with G, the latter being a new type of base pair between ionized thymine base and guanine base. In silico structural modeling suggests that the DNA polymerase can accept the reversed wobble pair with G, as well as the Watson-Crick pair with A.

Highlights

Hydroxyl radicals, activated from hydrogen peroxide and hydrogen superoxide anion under light radiation, are well known as potent mutagens that attack DNA and convert them to many different kinds of base and ribose derivatives [1, 2]
In order to establish the structural basis for such mutagenesis, the crystal structures of two kinds of DNA d(CGCGRATfUCGCG) with R = A/G have been determined by X-ray crystallography
The other abbreviations used are fU for 5-formyluracil or 2 -deoxy-5-formyluridine residue, dfUTP for 2 -deoxy5-formyluridine 5 -triphosphate, HPLC for high pressure liquid chromatography, fUA for d(CGCGAATfUCGCG), and fUG for d(CGCGGATfUCGCG).) It was demonstrated that 2 -deoxy-5-formyluridine triphosphate was incorporated against both A and G templates, possibly forming fU:A and fU:G base pairs during in vitro DNA replication [3, 4]

Summary

Introduction

Hydroxyl radicals, activated from hydrogen peroxide and hydrogen superoxide anion under light radiation, are well known as potent mutagens that attack DNA and convert them to many different kinds of base and ribose derivatives [1, 2]. When an excess amount of the radicals attacks DNA, the thymine base is oxidized at the 5-methyl group to form 5-formyluracil base (hereafter 2 deoxy-5-formyluridine residue is referred to as fU) as a major product. The other abbreviations used are fU for 5-formyluracil or 2 -deoxy-5-formyluridine residue, dfUTP for 2 -deoxy5-formyluridine 5 -triphosphate, HPLC for high pressure liquid chromatography, fUA for d(CGCGAATfUCGCG), and fUG for d(CGCGGATfUCGCG).) It was demonstrated that 2 -deoxy-5-formyluridine triphosphate (dfUTP) was incorporated against both A and G templates, possibly forming fU:A and fU:G base pairs during in vitro DNA replication [3, 4]. These results suggest that fU can behave as C, A, and G in addition to its original property of T

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