dc.contributor |
Háskóli Íslands |
dc.contributor |
University of Iceland |
dc.contributor.author |
Gophane, Dnyaneshwar B |
dc.contributor.author |
Sigurdsson, Snorri |
dc.date.accessioned |
2020-08-10T11:31:54Z |
dc.date.available |
2020-08-10T11:31:54Z |
dc.date.issued |
2015-02-09 |
dc.identifier.citation |
Gophane, D. B.; Sigurdsson, S. T. Beilstein J. Org. Chem. 2015, 11, 219–227. doi:10.3762/bjoc.11.24 |
dc.identifier.issn |
1860-5397 |
dc.identifier.uri |
https://hdl.handle.net/20.500.11815/1947 |
dc.description |
Publisher's version (útgefin grein) |
dc.description.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 formation 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. |
dc.description.sponsorship |
We thank the Icelandic Research Fund and the University of Iceland Research Fund for financial support (141062-951). We thank Dr. Pavol Cekan for technical assistance, Dr. Sigridur Jonsdottir for NMR and MS analyses and the members of the Sigurdsson research group for helpful discussions. |
dc.format.extent |
219-227 |
dc.language.iso |
en |
dc.publisher |
Beilstein Institut |
dc.relation.ispartofseries |
Beilstein J. Org. Chem.;11 |
dc.rights |
info:eu-repo/semantics/openAccess |
dc.subject |
Aminoxyl radical |
dc.subject |
ESR spectroscopy |
dc.subject |
Nitroxide |
dc.subject |
Nucleic acids |
dc.subject |
Site directed spin labeling |
dc.subject |
Spin labels |
dc.subject |
Structure dependent dynamics |
dc.subject |
Kjarnsýrur |
dc.subject |
Litrófsgreining |
dc.subject |
DNA kjarnsýra |
dc.title |
TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy |
dc.type |
info:eu-repo/semantics/article |
dcterms.license |
This is an Open Access article under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
dc.description.version |
Peer reviewed |
dc.identifier.journal |
Beilstein Journal of Organic Chemistry |
dc.identifier.doi |
10.3762/bjoc.11.24 |
dc.contributor.department |
Raunvísindadeild (HÍ) |
dc.contributor.department |
Faculty of Physical Sciences (UI) |
dc.contributor.department |
Raunvísindastofnun (HÍ) |
dc.contributor.department |
Science Institute (UI) |
dc.contributor.school |
Verkfræði- og náttúruvísindasvið (HÍ) |
dc.contributor.school |
School of Engineering and Natural Sciences (UI) |