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Nucleic Acids Research Advance Access originally published online on September 19, 2008
Nucleic Acids Research 2008 36(18):5946-5954; doi:10.1093/nar/gkn562
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Nucleic Acids Research, 2008, Vol. 36, No. 18 5946-5954
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Rigid spin-labeled nucleoside Ç: a nonperturbing EPR probe of nucleic acid conformation

Pavol Cekan1, Alyssa L. Smith2, Nivrutti Barhate2, Bruce H. Robinson2 and Snorri Th. Sigurdsson1,*

1University of Iceland, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland and 2Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA

*To whom correspondence should be addressed. Tel: +354 5 25 48 01; Fax: +354 5 52 89 11; Email: snorrisi{at}hi.is

Received June 16, 2008. Revised August 2, 2008. Accepted August 19, 2008.

Rigid spin-labeled nucleoside Ç, an analog of deoxycytidine that base-pairs with deoxyguanosine, was incorporated into DNA oligomers by chemical synthesis. Thermal denaturation experiments and circular dichroism (CD) measurements showed that Ç has a negligible effect on DNA duplex stability and conformation. Nucleoside Ç was incorporated into several positions within single-stranded DNA oligomers that can adopt two hairpin conformations of similar energy, each of which contains a four-base loop. The relative mobility of nucleotides in the alternating C/G hairpin loops, 5'-d(GCGC) and 5'-d(CGCG), was determined by electron paramagnetic resonance (EPR) spectroscopy. The most mobile nucleotide in the loop is the second one from the 5'-end, followed by the third, first and fourth nucleotides, consistent with previous NMR studies of DNA hairpin loops of different sequences. The EPR hairpin data were also corroborated by fluorescence spectroscopy using oligomers containing reduced Ç (Çf), which is fluorescent. Furthermore, EPR spectra of duplex DNAs that contained Ç at the end of the helix showed features that indicated dipolar coupling between two spins. These data are consistent with end-to-end duplex stacking in solution, which was only observed when G was paired to Ç, but not when Ç was paired with A, C or T.


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