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Biophys J, January 2000, p. 430-438, Vol. 78, No. 1

Dynamics and Ordering in a Spin-Labeled Oligonucleotide Observed by 220 GHz Electron Paramagnetic Resonance

David E. Budil,* Stephen V. Kolaczkowski,* Alex Perry,Dagger Chamakura Varaprasad,Dagger Francis Johnson,Dagger and Phyllis R. Straussdagger

Departments of  *Chemistry and  dagger Biology, Northeastern University, Boston, Massachusetts 02115; and  Dagger Department of Pharmacological Sciences, State University of New York at Stonybrook, Stonybrook, New York 11794 USA

The dynamics of a newly synthesized cytosine spin-label and the spin-labeled pentamer TTC*TT have been observed by high-frequency (220 GHz) electron paramagnetic resonance (EPR) in aqueous solution at ambient temperature using only nanomolar amounts of spin-label. Temperature studies were carried out for both labeled species in buffer containing glycerol. The motion of the spin-labeled monomer could be fitted using a model of fully anisotropic rotation (FAR) over the entire temperature range studied. In the single-stranded pentamer, the high-field spectra are best interpreted using a model of microscopic ordering with macroscopic disorder (MOMD) with the probe in a highly nonpolar environment. The observed local order parameters of 0.60-0.70 suggest a micelle-like structure in which the label is tightly packed with the hydrophobic bases. These preliminary studies illustrate how the excellent orientation selectivity of high-field EPR provides new dynamic information about local base motions in DNA, and also how high-field EPR of spin-labels allows one to discriminate accurately between the effects of local versus global motions in spin-labeled macromolecules.

Biophys J, January 2000, p. 430-438, Vol. 78, No. 1
© 2000 by the Biophysical Society   0006-3495/00/01/430/09  $2.00


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