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...

Full description

Bibliographic Details
Main Authors: Dnyaneshwar B. Gophane, Snorri Th. Sigurdsson
Format: Article
Language:English
Published: Beilstein-Institut 2015-02-01
Series:Beilstein Journal of Organic Chemistry
Subjects:
Online Access:https://doi.org/10.3762/bjoc.11.24
_version_ 1818735171674832896
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.
first_indexed 2024-12-18T00:17:01Z
format Article
id doaj.art-24c1f316ccbf44c4a25a4289c72425dd
institution Directory Open Access Journal
issn 1860-5397
language English
last_indexed 2024-12-18T00:17:01Z
publishDate 2015-02-01
publisher Beilstein-Institut
record_format Article
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