PELDOR analysis of enzyme-induced structural changes in damaged DNA duplexes

Molecular BioSystems Pub Date: 2011-07-06 DOI: 10.1039/C1MB05189J

Abstract

PELDOR (pulsed electron–electron double resonance) spectroscopy was applied to determine spin–spin distances in spin-labeled DNA duplexes (13-mer and 17-mer) containing the damaged sites 8-oxoguanine or uncleavable abasic site analogue tetrahydrofuran. The lesions were located in one strand of the DNA, and two nitroxyl spin labels were attached at the 5′- and 3′-ends of the complementary strand. PELDOR data allow us to obtain distances between the two spin labels in DNAs, which turned out to be around 5 nm for the 13-mer DNA and around 6 nm for 17-mer DNA. Results of PELDOR measurements were supported by molecular dynamics calculations. Study of the interaction of DNA fragments with DNA repair enzyme 8-oxoguanine-DNA glycosylase from E. coli (Fpg protein) showed that this interaction leads to a noticeable decrease of the distance between spin labels, which indicates the enzyme-induced bending of the DNA duplex. This bending may be important for the mechanisms of recognition of damaged sites by DNA repair enzymes.

Graphical abstract: PELDOR analysis of enzyme-induced structural changes in damaged DNA duplexes
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