Journal of the American Chemical Society
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Figure 3. A representation of the B-form helical DNA (Maes-
tro 10.5, Schrödinger, LLC). The A-strand backbone is shown
in green and the B-strand in blue. Labeled positions are rep-
resented in orange. Modal distances from DEER distance
measurements (see Figure 2) and powder CW EPR spectra
(denoted *) are shown. Distances in brackets were measured
between the 2 -hydroxyl O atoms of the model (Pymol 1.4,
Schrödinger, LLC).
In conclusion, we have developed a sequence-flexible
method for oligonucleotide spin labeling. 2 -Alkynyl-
nucleosides were incorporated into a 16-mer DNA duplex at
various positions using standard solid phase synthesis, and
functionalized with a range of azide-containing nitroxides.
Pulsed and CW EPR experiments were used to determine
dynamic and electron spin relaxation properties of the labels,
and to measure interspin distances, with the structure of the
radical probe influencing the positioning of the spin label on
the duplex. The structural information obtained demon-
strates the versatility of this approach in exploring the struc-
ture of nucleic acids, including applications beyond SDSL.
ASSOCIATED CONTENT
Supporting Information
(7) (a) Sukeda, M.; Ichikawa, S.; Matsuda, A.; Shuto, S. Angew.
Chem. Int. Ed. 2002, 41, 4748; (b) Sukeda, M.; Ichikawa, S.; Matsuda,
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Matui, C. J. Org. Chem. 1999, 64, 8024.
(9) Divakar, K. J.; Reese, C. B. J. Chem. Soc. Perkin Trans. 1 1982,
1171.
(10) See the Supporting Information for details.
Supporting Information: Experimental conditions, copies of
spectroscopic data, characterization of oligonucleotides.
Corresponding Authors
tom.brown@chem.ox.ac.uk;
ed-
ward.anderson@chem.ox.ac.uk; jel20@st-andrews.ac.uk
(11) Couet, W. R. R.; Brasch, R. C. C.; Sosnovsky, C.; Lukszo, J.;
Prakash, I.; Gnewech, C. T. T.; Tozer, T. N. N. Tetrahedron 1985, 41,
1165.
Notes
The authors declare no competing financial interests.
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Y.; Takeshita, K.; Eaton, S. S.; Eaton, G. R. Chem. Commun. 2009,
454; (b) Kirilyuk, I. A.; Polienko, Y. F.; Krumkacheva, O. A.;
Strizhakov, R. K.; Gatilov, Y. V.; Grigor'ev, I. A.; Bagryanskaya, E. G.
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ACKNOWLEDGMENT
TB and AHE-S thank the BBSRC (sLOLA grant
BB/J001694/1). EAA thanks the EPSRC (EP/K005391/1,
EP/M019195/1). JEL thanks the EPSRC (EP/LO22044/1), and
the Royal Society for a University Research Fellowship and
grant RF120645. We thank the Wellcome Trust for the Q-
band EPR spectrometer (099149/Z/12/Z), the EPSRC National
EPR Service for spectrometer time, and Dr Hassane El Mka-
mi for technical assistance.
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