Methods to selectively introduce radicals into DNA [Elektronische Ressource] : an EPR spectroscopic study / von Emiliano Feresin

Emilianof

Informations

• Publié par: goethe_universitat_frankfurt_am_main
• Publié le: 01 janvier 2005
• Nombre de lectures: 35
• Poids de l'ouvrage: 3 Mo

Extrait

Methods to Selectively Introduce Radicals into DNA.
An EPR spectroscopic Study.


Dissertation
zur Erlangung des Doktorgrades
der Naturwissenschaften



vorgelegt beim Fachbereich
“Chemische und Pharmazeutische Wissenschaften“
der Johann Wolfgang Goethe - Universität
in Frankfurt am Main



von
Emiliano Feresin
aus Aiello del Friuli, Udine (Italien)


Frankfurt (2004)
(DF1)
















Vom Fachbereich 14 “Chemische und Pharmazeutische Wissenschaften“
der Johann Wolfgang Goethe - Universität als Dissertation angenommen.




Dekan: Prof. Dr. H. Schwalbe
Gutachter: Prof. Dr. T. F. Prisner
P.D. Dr. O. Schiemann
Datum der Disputation: 21. September 2004





Fatti non foste a viver come bruti
ma per seguir virtute e conoscenza
(Dante, Divina)













Table of Contents

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Table of Contents

Symbols and Abbreviations

Introduction………………………………………………………………………. 1
Aim of the Thesis…………………………………………….... 1Scientific Contributions………………………………………... 3

Chapter 1. DNA and Electron Transfer…………………………………. 5
1.1 The DNA Double Helix: Structure and Function……………… 5
1.2 Electron Transfer Processes in DNA….……………..………... 8
1.2.1 Unselective high-energy ionization of DNA detected
by EPR…………………………………………………. 9
1.2.2 Selective radical formation in DNA by photoinduced
Electron Transfer…………..…………………………... 11
1.2.3 Mechanistic picture for hole transfer in DNA…………. 16
1.2.3a Superexchange………………………………….. 17
1.2.3b Hopping mechanism between guanines………... 19
1.2.3c Hopping m between adenines………… 20
1.2.3d Polaron assisted mechanism……………….…… 21
1.2.3e Proton coupled electron transfer………………... 21
1.2.4 Excess Electron Transfer in DNA……………………... 22
1.2.5 Biradicals in DNA? Possible correlation between
charge transfer rate and exchange coupling…………… 23
1.3 References…………………………………………………….. 25

Chapter 2. EPR Theory and Model Spectra………………………….... 31
2.1 Introduction…………………………………………….……... 31
2.2 Spin and Zeeman interaction…………………………………. 32
2.3 Static Spin Hamiltonian and its Components…….…………... 36
2.3.1 The g tensor……………………………………….….. 37
2.3.2 The hyperfine tensor………………………………….. 39Table of Contents

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2.4 Spectral Analysis of Isotropic Hyperfine Patterns………….…. 42
2.4.1 π-type organic radicals: spin density and spin
polarization ………………………………….….…….. 422.4.2 Tert-butyl radical: hyperconiugation………..…….…… 442.4.3 The thymyl radical……………………..……………… 48
2.5 Relaxation Phenomena…...……………………………………. 50
2.6 Cw X-Band EPR Spectrometer……………………………...… 54
2.7 References……………………………………………………... 55

Chapter 3. EPR Spectroscopic Study of Novel Aromatic Nitroxides as
Potential DNA Intercalators …………………………….…. 57
3.1 Materials and Methods………………………………………… 58
3.1.1 Sample preparation……………………………..……… 58
3.1.2 Simulation and fit program……..………………..……. 58
3.2 Results and Discussion……...……………………………….… 59
3.2.1 EPR spectroscopy and simulations of the experimental
spectra………………………………………………….. 59
3.2.2 DFT calculations……………………….……………… 62
3.3 Conclusions……………………………………………………. 65
3.4 References……………………………………………………... 65

Chapter 4. EPR Detection of Selectively Generated Guanine Radicals
67in DNA……...……………………………………………….…
4.1 Materials and Methods………………………………………… 67
4.1.1 Sample preparation and irradiation………………….… 67
4.1.2 The flash quench-technique…………………………… 68
4.2 Results and Conclusions……………………………………….. 69
4.3 References……………………………………………………... 71

Chapter 5. The 4'-Pivaloyl Substituted Thymidine as Precursor for the
Thymyl Radical………………………………………………. 73
5.1 Materials and Methods………………………………………… 74 Table of Contents

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5.1.1 Sample preparation…………………………………….. 74
5.1.2 Generation of radicals by UV Irradiation……………… 76
5.1.3 Photolysis of the pivaloyl group and radical formation.. 76
5.1.4 Component differentiation of composite EPR spectra… 78
5.2 Results…………………………………………………………. 79
5.2.1 Sample dissolved in CHCN…………………………... 793
5.2.2 Sample dissolved in H 0 and in DO………………….. 822 2
5.2.3 Simulations and computer reconstructions………….… 85
5.2.4 Double strand DNA modified with the nucleotide
derivative of 1……………………………………….…. 88
5.3 Discussion and Conclusions………………………………....… 89
5.3.1 Components and radical structures………………….… 89
5.3.2 Mechanism of radical formation…………………….… 92
5.3.3 Discussion about the modified double strand
DNA………………………………………….………... 94
5.4 References……………………………………………………... 95

Chapter 6. A New Modified Thymidine as Precursor for a Thymine
Based Radical and as Electron Injector into DNA…………. 99
6.1 Materials and Methods………………………………………… 100
6.1.1 Sample preparation…………………………………….. 100
6.1.2 Generation of radicals by UV Irradiation……………… 100
6.2 Results…………………………………………………………. 100
6.2.1 Sample dissolved in H 0 and DO……………………... 1002 2
6.2.2 Sample dissolved in CHCN…………………………... 1033
6.2.3 Simulations and computer reconstruction of
experimental spectra…………………………………… 106
6.3 Discussion and Conclusions…………………...…………….… 109
6.4 References……………………………………………………... 113

Summary and Outlook..……………………………………………………….…. 115Table of Contents

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Zusammenfassung und Ausblick........…………………………………………... 121
Appendix A…………………………………………………………………….…. 127
Appendix B…………………………………………………………………….….. 131
Lebenslauf………..……………………………………………………………….. 133
Acknowledgements
Symbols and abbreviations

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SYMBOLS AND ABBREVIATIONS

A Adenine
a isotropic hyperfine coupling iso
a.u. arbitrary units
C Cytosine
CT Charge Transfer
cw continuous wave
DFT Density Functional Theory
DNA DeoxyriboNucleic Acid
DPPH ( α,α’)-diphenyl- β-picrylhydrazyl
ENDOR Electron Nuclear Double Resonance
EPR Electron Paramagnetic Resonance
ESEEM Electron Spin-Echo Envelope Modulation spectroscopy
ET Electron Transfer
Fig. Figure
g Free electron g-factor e
gNuclear g-factor N
G Gauss Guanine
hf hyperfine
HPLC High Performance Liquid Chromatography
I Inosine Intensity
Lw linewidth
m.f. molecular formula
mw microwave
NHE Nerst Hydrogen Electrode
PELDOR Pulsed Electron Double Resonance
RT Room Temperature (25 °C)
T Thymine
UV Ultra Violet
vis visible