Structural changes of an abasic site in duplex DNA affect noncovalent binding of the spin label Ç

Sandip A. Shelke, Snorri Th Sigurdsson*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

17 Citations (Scopus)

Abstract

The influence of structural changes of an abasic site in duplex DNA on noncovalent and site-directed spin labeling (NC-SDSL) of the spin label Ç were examined with electron paramagnetic resonance (EPR) spectroscopy. The binding affinities of Ç to sixteen different DNA duplexes containing all possible sequences immediately flanking the abasic site were determined and the results showed that the binding of Ç is highly flanking-sequence dependent. In general, a 5′-dG nucleotide favors the binding of the spin label. In particular, 5′-d(G-T) was the best binding sequence whereas 5′-d(C-T) showed the lowest affinity. Changing the structure of the abasic site linker from a tetrahydrofuran analog (F) to the anucleosidic C 3-spacer (C3) does not appreciably affect the binding of Ç to the abasic site. For efficient binding of Ç, the abasic site needs to be located at least four base pairs away from the duplex end. Introducing a methyl substituent at N3 of Ç did not change the binding affinity, but a decreased binding was observed for both N3-ethyl and-propyl groups. These results will guide the design of abasic site receptors and spin label ligands for NC-SDSL of nucleic acids.

Original languageEnglish
Pages (from-to)3732-3740
Number of pages9
JournalNucleic Acids Research
Volume40
Issue number8
DOIs
Publication statusPublished - Apr 2012

Bibliographical note

Funding Information:
Icelandic Research Fund (110035021); University of Iceland Research Fund (a doctoral fellowship to S.A.S.). Funding for open access charge: Science Institute, University of Iceland.

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