TEMPO-derived spin labels linked to the nucleobases adenine
and cytosine for probing local structural perturbations in DNA
by EPR spectroscopy
Dnyaneshwar B. Gophane and Snorri Th. Sigurdsson*
Full Research Paper
Address:
University of Iceland, Department of Chemistry, Science Institute,
Dunhaga 3, 107 Reykjavik, Iceland
Received: 18 November 2014
Accepted: 15 January 2015
Published: 09 February 2015
Email:
*
Corresponding author
This article is part of the Thematic Series "Nucleic acid chemistry".
Guest Editor: H.-A. Wagenknecht
Keywords:
aminoxyl radical; ESR spectroscopy; nitroxide; nucleic acids;
site-directed spin labeling (SDSL); spin labels; structure-dependent
dynamics
© 2015 Gophane and Sigurdsson; licensee Beilstein-Institut.
License and terms: see end of document.
Abstract
Three 2´-deoxynucleosides containing semi-flexible spin labels, namely TA, UA and UC, were prepared and incorporated into
deoxyoligonucleotides using the phosphoramidite method. All three nucleosides contain 2,2,6,6-tetramethylpiperidine-1-oxyl
(
TEMPO) connected to the exocyclic amino group; TA directly and UA as well as UC through a urea linkage. TA and UC showed a
minor destabilization of a DNA duplex, as registered by a small decrease in the melting temperature, while UA destabilized the
duplex by more than 10 °C. Circular dichroism (CD) measurements indicated that all three labels were accommodated in B-DNA
duplex. The mobility of the spin label TA varied with different base-pairing partners in duplex DNA, with the TA•T pair being the
least mobile. Furthermore, TA showed decreased mobility under acidic conditions for the sequences TA•C and TA•G, to the extent
that the EPR spectrum of the latter became nearly superimposable to that of TA•T. The reduced mobility of the TA•C and TA•G
mismatches at pH 5 is consistent with the formation of TAH+•C and TAH+•G, in which protonation of N1 of A allows the forma-
tion of an additional hydrogen bond to N3 of C and N7 of G, respectively, with G in a syn-conformation. The urea-based spin labels
UA and UC were more mobile than TA, but still showed a minor variation in their EPR spectra when paired with A, G, C or T in a
DNA duplex. UA and UC had similar mobility order for the different base pairs, with the lowest mobility when paired with C and
the highest when paired with T.
Introduction
The knowledge about structures and conformational dynamics mation can be obtained by X-ray crystallography [1-6] and
of nucleic acids, as well as other biomolecules, is essential to nuclear magnetic resonance (NMR) spectroscopy [7-12]. Elec-
understand their biological functions, including interactions tron paramagnetic resonance (EPR) and fluorescence spectro-
with other molecules. The exact atom-to-atom structural infor- scopies are nowadays routinely used to study global structures
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