scholarly journals The Internal Dynamics of Mini c TAR DNA Probed by Electron Paramagnetic Resonance of Nitroxide Spin-Labels at the Lower Stem, the Loop, and the Bulge

Biochemistry ◽  
2012 ◽  
Vol 51 (43) ◽  
pp. 8530-8541 ◽  
Author(s):  
Yan Sun ◽  
Ziwei Zhang ◽  
Vladimir M. Grigoryants ◽  
William K. Myers ◽  
Fei Liu ◽  
...  
Keyword(s):  
Electron Paramagnetic Resonance ◽  
Spin Labels ◽  
Internal Dynamics ◽  
Paramagnetic Resonance ◽  
Nitroxide Spin Labels ◽  
Electron Paramagnetic ◽  
Lower Stem

scholarly journals Triarylmethyl Radicals: An EPR Study of 13C Hyperfine Coupling Constants

2017 ◽  
Vol 231 (4) ◽  
Author(s):  
Andrey A. Kuzhelev ◽  
Victor M. Tormyshev ◽  
Olga Yu. Rogozhnikova ◽  
Dmitry V. Trukhin ◽  
Tatiana I. Troitskaya ◽  
...  
Keyword(s):  
Electron Paramagnetic Resonance ◽  
Epr Spectroscopy ◽  
Hyperfine Coupling ◽  
Coupling Constants ◽  
Spin Labels ◽  
Spin Probes ◽  
Paramagnetic Resonance ◽  
Hyperfine Coupling Constants ◽  
Electron Paramagnetic ◽  
Triarylmethyl Radicals

AbstractTriarylmethyl (TAM) radicals are widely used in electron paramagnetic resonance (EPR) spectroscopy as spin labels and in EPR imaging as spin probes for

scholarly journals DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling

2019 ◽  
Vol 47 (15) ◽  
pp. 7767-7780 ◽  
Author(s):  
Olesya A Krumkacheva ◽  
Georgiy Yu Shevelev ◽  
Alexander A Lomzov ◽  
Nadezhda S Dyrkheeva ◽  
Andrey A Kuzhelev ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Md Simulations ◽  
Dna Lesions ◽  
Spin Labels ◽  
Paramagnetic Resonance ◽  
Applied Pulse ◽  
Oligonucleotide Duplex ◽  
Nitroxide Spin Labels ◽  
Ap Sites ◽  
Electron Paramagnetic

Abstract A DNA molecule is under continuous influence of endogenous and exogenous damaging factors, which produce a variety of DNA lesions. Apurinic/apyrimidinic sites (abasic or AP sites) are among the most common DNA lesions. In this work, we applied pulse dipolar electron paramagnetic resonance (EPR) spectroscopy in combination with molecular dynamics (MD) simulations to investigate in-depth conformational changes in DNA containing an AP site and in a complex of this DNA with AP endonuclease 1 (APE1). For this purpose, triarylmethyl (TAM)-based spin labels were attached to the 5′ ends of an oligonucleotide duplex, and nitroxide spin labels were introduced into APE1. In this way, we created a system that enabled monitoring the conformational changes of the main APE1 substrate by EPR. In addition, we were able to trace substrate-to-product transformation in this system. The use of different (orthogonal) spin labels in the enzyme and in the DNA substrate has a crucial advantage allowing for detailed investigation of local damage and conformational changes in AP-DNA alone and in its complex with APE1.

Nitroxides and nucleic acids: Chemistry and electron paramagnetic resonance (EPR) spectroscopy

2011 ◽  
Vol 83 (3) ◽  
pp. 677-686 ◽  
Author(s):  
Snorri Th. Sigurdsson
Keyword(s):  
Electron Paramagnetic Resonance ◽  
Nucleic Acids ◽  
Epr Spectroscopy ◽  
Noncovalent Interactions ◽  
Spin Labeling ◽  
Structural Features ◽  
Spin Labels ◽  
Abasic Site ◽  
Paramagnetic Resonance ◽  
Electron Paramagnetic

Electron paramagnetic resonance (EPR) spectroscopy has increasingly been applied for the study of nucleic acid structure and dynamics. Such studies require incorporation of free radicals (spin labels) into the biopolymer. The labels can be incorporated during chemical synthesis of the oligomer (phosphoramidite approach) or postsynthetically, by reaction of a spin-labeling reagent with a reactive functional group on the oligonucleotide. Incorporation of the rigid nitroxide spin label Ç is an example of the phosphoramidite method, and reaction of a spin-labeled azide with an alkyne-modified oligomer to yield a triazole-derived, spin-labeled nucleotide illustrates the postsynthetic spin-labeling strategy. Characterization and application of these labels to study structural features of DNA by EPR spectroscopy is discussed. Finally, a new spin-labeling strategy is described for nucleic acids that relies on noncovalent interactions between a spin-labeled nucleobase and an abasic site in duplex DNA.

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