TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy
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 dire...
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Beilstein-Institut
2015-02-01
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Series: | Beilstein Journal of Organic Chemistry |
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Online Access: | https://doi.org/10.3762/bjoc.11.24 |
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author | Dnyaneshwar B. Gophane Snorri Th. Sigurdsson |
author_facet | Dnyaneshwar B. Gophane Snorri Th. Sigurdsson |
author_sort | Dnyaneshwar B. Gophane |
collection | DOAJ |
description | 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. |
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institution | Directory Open Access Journal |
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language | English |
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series | Beilstein Journal of Organic Chemistry |
spelling | doaj.art-24c1f316ccbf44c4a25a4289c72425dd2022-12-21T21:27:29ZengBeilstein-InstitutBeilstein Journal of Organic Chemistry1860-53972015-02-0111121922710.3762/bjoc.11.241860-5397-11-24TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopyDnyaneshwar B. Gophane0Snorri Th. Sigurdsson1University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, IcelandUniversity of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, IcelandThree 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.https://doi.org/10.3762/bjoc.11.24aminoxyl radicalESR spectroscopynitroxidenucleic acidssite-directed spin labeling (SDSL)spin labelsstructure-dependent dynamics |
spellingShingle | Dnyaneshwar B. Gophane Snorri Th. Sigurdsson TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy Beilstein Journal of Organic Chemistry aminoxyl radical ESR spectroscopy nitroxide nucleic acids site-directed spin labeling (SDSL) spin labels structure-dependent dynamics |
title | TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy |
title_full | TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy |
title_fullStr | TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy |
title_full_unstemmed | TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy |
title_short | TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy |
title_sort | tempo derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in dna by epr spectroscopy |
topic | aminoxyl radical ESR spectroscopy nitroxide nucleic acids site-directed spin labeling (SDSL) spin labels structure-dependent dynamics |
url | https://doi.org/10.3762/bjoc.11.24 |
work_keys_str_mv | AT dnyaneshwarbgophane tempoderivedspinlabelslinkedtothenucleobasesadenineandcytosineforprobinglocalstructuralperturbationsindnabyeprspectroscopy AT snorrithsigurdsson tempoderivedspinlabelslinkedtothenucleobasesadenineandcytosineforprobinglocalstructuralperturbationsindnabyeprspectroscopy |