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

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.