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π –stacking effects on the EPR parameters of a prototypical DNA spin label
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0002-1763-9383
2013 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 25, 10466-10471 p.Article in journal (Refereed) Published
Abstract [en]

The character and value of spin labels for probing environments like double-stranded DNA depends on the degree of changeof the spin Hamiltonian parameters of the spin label induced by the environment. Herein we provide a systematic theoreticalinvestigation of this issue, based on a density functional theory method applied to a spin labeled DNA model system, focusingon the dependence of the EPR properties of the spin label on the π stacking and hydrogen bonding that occur upon incorporatingthe spin label into selected base pair inside DNA. It is found that the EPR spin Hamiltonian parameters of the spin label is onlynegligibly affected by its incorporation into DNA, when compared to the its free form. This result gives theoretical ground forthe common empirical assumption regarding the behaviour of spin Hamiltonian parameters made in EPR based measurementsof distance between spin labels incorporated into DNA.

Place, publisher, year, edition, pages
RSC Publishing, 2013. Vol. 15, no 25, 10466-10471 p.
Keyword [en]
EPR, spin labels, DNA
National Category
Theoretical Chemistry
Research subject
SRA - E-Science (SeRC)
URN: urn:nbn:se:kth:diva-119514DOI: 10.1039/C3CP51129DISI: 000319943200050ScopusID: 2-s2.0-84881088674OAI: diva2:611235
EU, FP7, Seventh Framework Programme, RI-283493Swedish e‐Science Research Center

This work was granted access to the HPC resources of MonteRosa/Swiss National High-Performance Centre made avail-able within the Distributed European Computing Initiative bythe PRACE-2IP, receiving funding from the European Com-munity Seventh Framework Programme (FP7/2007-2013) un-der grant agreement no. RI-283493.

QC 20130422

Available from: 2013-05-07 Created: 2013-03-15 Last updated: 2013-12-11Bibliographically approved
In thesis
1. Theoretical studies of EPR parameters of spin-labels incomplex environments
Open this publication in new window or tab >>Theoretical studies of EPR parameters of spin-labels incomplex environments
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis encloses quantum chemical calculations performed in the framework of density functional response theory for evaluating electron paramagnetic resonance (EPR) spin Hamiltonian parameters of various spin-labels in different environments. These parameters are the well known electronic g-tensor and the nitrogen hyperfine coupling constants, which are extensively explored in this work for various systems. A special attention was devoted to the relationships that form between the structural and spectroscopic properties that can be accounted for as an environmental inuence. Such environmental effects were addressed either within a fully quantum mechanical formalism, involving simplified model structures that still capture the physical properties of the extended system, or by employing a quantum mechanics/molecular mechanics (QM/MM) approach. The latter implies that the nitroxide spin label is treated quantum mechanically, while the environment is treated in a classical discrete manner, with appropriate force fields employed for its description. The state-of- the art techniques employed in this work allow for an optimum accounting of the environmental effects that play an important role for the behaviour of EPR properties of nitroxides spin labels. One achievement presented in this thesis includes the first theoretical con_rmation of an empirical assumption that is usually made for inter-molecular distance measurement experiments in deoxyribonucleic acid (DNA), involving pulsed electron-electron double resonance (PELDOR) and site-directed spin labeling (SDSL) techniques. This refers to the fact that the EPR parameters of the spin-labels are not affected by their interaction with the nucleobases from which DNA is constituted. Another important result presented deals with the inuence of a supramolecular complex on the EPR properties of an encapsulated nitroxide spin-label. The enclusion complex affects the hydrogen bonding topology that forms around the R2NO moiety of the nitroxide. This, on the other hand has a major impact on its structure which further on governs the magnitude of the spectroscopic properties. The projects and results presented in this thesis offer an example of successful usage of modern quantum chemistry techniques for the investigation of EPR parameters of spin-labels in complex systems.


Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2013. iv, 57 p.
Trita-BIO-Report, ISSN 1654-2312 ; 2013:6
EPR, DFT, spin-labels, QM/MM, Breit-Pauli Hamiltonian
National Category
Theoretical Chemistry
urn:nbn:se:kth:diva-119515 (URN)978-91-7501-681-8 (ISBN)
Public defence
2013-04-05, FB 54, AlbaNova University Center, Stockholm, 10:00 (English)

QC 20130318

Available from: 2013-03-18 Created: 2013-03-15 Last updated: 2013-03-18Bibliographically approved

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