ESR and ESR microscopy in geosciences and radiation dosimetry

ESR and its microscopic imaging (microscopy) have found new applications in interdisciplinary fields related with geosciences and with radiation dosimetry. Geological, archaeological and forensic dating has been made through paleo-dosimetry of natural radiation and chemical reactions of both radical formation and valency changes. ESR microscopy, especially the simple scanning method has a potentiality to be used in various fields. New applications of ESR are briefly reviewed with some examples.     

Photo-CIDNP study of the splitting of the dinucleotidecis,syn-thymine dimer with reduced flavin as a sensitizer: Evidence for a thymine radical anion intermediate

Photochemically induced dynamic nuclear polarization (photo-CIDNP) studies were performed on the splitting ofcis,syn 2′-deoxythymidylyl-(3′→5′)-2′-deoxythymidine cyclobutane dimer (cs-dTp dT), using reduced flavin as a sensitizer. This system serves as a model for the light-induced repair mechanism of thymine dimers in DNA by the enzyme photolyase. The CIDNP spectrum shows enhanced absorption of the two C6-H protons of the corresponding monomer dTpdT, which demonstrates that a thymine radical anion is involved in the splitting of the dimer. This is supported by a similar CIDNP spectrum that is obtained with the electron-donorN _α-acetyl tryptophan as a sensitizer. This result suggests that the light-induced splitting of thymine dimers in DNA by photolyase also proceedsvia the thymine radical anion. The small difference in intensity of the two CIDNP signals belonging to the C6-H protons shows that the unpaired electron in the monomer radical has a slight preference for the thymine moiety at the 5′ terminus.     

ESR and ENDOR experiments using a disc-shaped resonator working in the Whispering Gallery Mode (WGM)

Different instrumental apparatuses are presented employing disc-shaped dielectric resonators working in the Whispering Gallery Mode (WGM). The conditions suitable to take the best from the microwave power obtained from a trade klystron in the X-band have been verified for the ESR part of the experiments. It is well known that a good ESR saturation condition is an essential prerequisite to have satisfactory ENDOR results. The WGM dielectric resonators seem to be very suitable for multiple irradiation purposes and in particular for ENDOR experiments which is the aspect we wanted to exploit here. Various radiofrequency ENDOR irradiation circuits have been tested and the obtained spectra of a γ-irradiated single crystal are presented and criticized. Some results for very high frequency ESR applications are also reported.     

Observation of broad EPR spectra of transient free radicals by FT-EPR

Application of electron spin echo Fourier transform EPR (ESE-FT-EPR) to photo-induced chemical reactions is presented. Main purpose of this study is to observe broad EPR spectra of free radicals having very shortT ₂ ^* by means of the ESE-FT-EPR technique. Details of the experimental procedures are described. In ESE experiments design of the resonator is important to obtain sufficient spectral bandwidth because of use of multiple pulses which decrease the bandwidth. We designed and constructed Loop-Gap-Resonantors (LGR) for light irradiation experiments and their specifications were examined. The phase cycling method is essential to obtain pure ESE signals and proper time resolution by eliminating unwanted FID signals which result from imperfect pulse angles. We applied this technique to observe the photo-induced electron transfer reaction between tetraphenylporphinato zinc(II) (ZnTPP) and duroquinone (DQ) in an ethanol solution, and successfully observed the time resolved EPR spectra of the both Zn(TPP) cation and DQ anion radicals by ESE-FT-EPR of the Hahn echo. The half-height full-width of envelope of EPR spectrum of Zn(TPP)⁺, which is never observed in ordinary FT-EPR, is about 16 MHz. Specificity of spectra and the time resolution are compared among the ESE-FT-, FT- and cw-Time-Resolved-EPR (cw-TREPR) techniques.     

Nucleic acid spin labeling study of interaction between polyadenylic acid: Polyuridilic acid duplex and egg phosphatidylcholine vesicles. Involvement of terminal and internal nucleotides and sugar-phosphate backbone

Model DNA-membrane contacts were studied in the system containing polyadenylic acid (polyA): polyuridilic acid (polyU) duplex and egg phosphatidylcholine (PC) vesicles without or in the presence of MgCl₂. PolyU containing O-(1-oxyl-2,2,5,5-tetramethylpyrroline-3-carbonyl) spin label at 2′-OH moiety was used for spin labeling study of nucleic acid-phospholipid interactions. For polyA labeled with the same nitroxyl radical EPR spectra from spin labels attached at terminal and at internal nucleotide units contribute into the EPR spectrum of d.s. polynucleotide without or in the presence of egg PC vesicles and Mg ions. Internal spin labels are more sensitive to the interaction with PC-MLV than terminal ones. The complexation between s.s. polynucleotide and PC-MLV was shown. The values of spin labels’ melting temperature of polyA: SL-polyU duplex at 1 mM MgCl₂ reflect the changes in rotational mobility of terminal spin labels connected with duplex→triplex transition. Arrhenius plots of temperature dependence of EPR spectra parameters prove that ribose moieties of sugarphosphate backbone are involved into the interaction between polynucleotide duplex and phospholipid bilayer. Egg PC vesicles demonstrate stabilizing effect on polyA: polyU duplex at 1 mM of Mg²⁺ and destabilizing effect at 5 mM Mg²⁺.     

Electron spin relaxation of some alkane cation radicals as an indicator of dynamics between the distorted structures

ESR saturation phenomenon was observed for various alkane cation radicals derived from cyclohexane, propane and norbornane in frozen halocarbon matrices at 4 K. In addition to spectral diffusion by spin-spin interaction between the radicals, which is a common mechanism of ESR relaxation in the solid state, isotropic hyperfine modulation by the dynamics between the equivalent distorted structures was found to be very important for those centers which show Jahn-Teller (JT) or pseudo-JT effects. The effect of annealing of the sample at 77 K is also discussed.     

Inosine — Adenosine base pairing in d-GGTACIAGTACC: Duplex and hairpin with a two-base loop

An oligonucleotide dodecamer d-GGTACIAGTACC containing two inosine-adenosine mismatched base-pairs has been studied by¹H and³¹P NMR spectroscopy. Unique assignments of¹H and³¹P spins have been achieved by using a recently proposed two-dimensionalheteronuclearlong rangecorrelation (2D-HELCO) technique. The 2D nuclear Overhauser enhancement spectroscopy (NOESY) spectrum recorded in a mixed solvent of 90% H₂O+10%²H₂O has been used to assign all the exchangeable imino and amino proton resonances. NMR results indicate that at concentrations above 5 mM, the molecule adopts a duplex structure where the inosine imino protons are hydrogen bonded. Cross-strand NOEs between the imino proton of I6 and H2 proton of A7 and that between H2 of I6 and H2 of A7 provide evidence for inosine-adenosine base-pairing, with both bases I6 and A7 inanti conformation. The observed NOE connectivitiesd1,d2 andd3 from almost the middle of the molecule to the two ends are consistent with a right handed B-DNA conformation. However, the molecule adopts a more extended conformation in the mismatch region to accomodate the bulky purine-purine (IA) base pairs. NMR experiments at lower concentrations indicate the coexistence of a monomeric hairpin with a two base loop, consisting of I6 and A7 units, in equilibrium with the duplex. 2D-ROESY experiment at such a concentration shows that the conformation of the stem of the hairpin does not deviate much from the corresponding region of the duplex and four nucleotides C5, I6, A7 and G8 undergo significant structural changes during the formation of hairpin loop.     

Statistical analysis of DNA duplex structures in solution derived by high resolution NMR

An initial statistical analysis has been performed on the helical parameters for the solution structures of three DNA duplexes recently solved in this laboratory by proton NMR. Local conformations in these structures belong to the B family of forms; nevertheless they display a strong sequence-dependent heterogeneity akin to that found in single crystals and by theoretical calculations. However, average helical parameters as well as their variations are quite different for short DNA fragments in solution and in crystal. Average helical twist in three NMR-refined oligonucleotides is 34.6°, in remarkable agreement with independent solution-state data, while helical twist is 36° for DNA in crystals. Other characteristic features of solution DNA conformations are negative slide, systematically open minor groove (for almost all sequences), and decreased helical rise. The latter, rather unexpected finding, is correlated with a surprisingly strong non-flatness of Watson-Crick base pairs. Deviations of base pairs from planarity proved to be a significant source of conformational variability; of particular importance is base stagger, which is often missed in structural analysis of DNA. Several new structural parameters have been introduced for dinucleotide steps, characterizing non-planar geometries of constituent base pairs; these parameters show a significant degree of correlation with traditional step parameters (twist, tillt roll, shift, slide, rise). Many sequence-dependent features are observed in solution structures; variation of roll and slide parameters occurs according to “Calladine’s rules”, while variation of helical twist appears to oppose them. However, a larger set of solution structures is needed to complete the analysis of sequence dependence of DNA conformation.     

Interactions between polyamines and nucleotides studied by31P and1H NMR

The formation of complexes between poly- and mono-amines and some polyphosphate molecules such as ATP, ADP and tripolyphosphate was studied by³¹P and¹H NMR. Evidence for formation of complexes was obtained by¹H NMR, while the values of dissociation constants of the complexes between nucleotides and spermine and spermidine, calculated from the shift of the³¹P NMR, were in mM range.     

Electron spin polarization of doublet state species due to interaction with excited triplet states in single crystals

Doublet states species trapped in crystalline solids show transient spin polarized EPR spectra if the crystal is illuminated by visible or UV light. The spin polarization is accounted for by the interaction of the doublet species with photoexcited triplet states. The mechanism of the process producing the spin polarization is examined and some experimental examples are discussed. The analysis of the time evolution of the transient variation of the EPR signal allows the measurements of the spin lattice relaxation time and in some cases of the diffusion rate of mobile triplet excitations in the crystal lattice.     

31P NMR studies on the interaction of morpholinyl anthracyclines and related compounds with d(CGTACG)2. Thermodynamic and kinetic parameters

³¹P NMR spectroscopy has been used to study the intercalation of the anthracyclines doxorubicin1, daunorubicin2, 4-demethoxydaunorubicin3, morpholinodoxorubicin4, methoxymorpholinodoxorubicin5 and 9-deoxydaunorubicin6 with the DNA fragment d(CGTACG)₂. The individual phosphate resonances of the oligonucleotide were assigned in the free as well as in the intercalated species. The³¹P chemical shift variations allowed us to identify the intercalation sites, which resulted to be the same for all compoundsi.e. between the terminal CG base-pairs of the helix (two molecules of drugper duplex). The binding constants, the dissociation rate constants and ΔG ^# values have been determined in different conditions of ionic strength and temperature. The kinetic constant (k _off) of the slow step of the anthracycline/duplex intercalation process has been directly measured by NOE exchange techniques. Binding constants depend on the ionic strength and on the self-association process so greatly, that their use to study by NMR anthracycline/DNA interactions is questionable. On the contrary, thek _off are not affected by these phenomena and present an interesting trend for1–6, thus showing that the average lifetime of the drug in the intercalation site appears to be important for determining the cytotoxicity and the antimitotic activity.     

Photoinduced reactions of covalently linked porphyrin quinones in reversed micelles as studied by EPR spectroscopy

From covalently linked porphyrin quinones, dissolved in reversed micellar solutions, porphyrin radical cations and semiquinone radical anions can be generated photochemically. At pH 7 of the water pool the radical species are rather short-lived and can thus only be observed duringin-situ light irradiation (optical pumping) of the sample. Different polarization patterns are observed in different types of micelles, e.g., CTAB cationic or Triton X-100 neutral reversed micelles. Specifically, in the former absorptive (either Boltzmann relaxed or enhanced absorptive) spectra are obtained, whereas in the latter both species (porphyrin radical cation and semiquinone radical anion) occur in emission. Complete emission is indicative of a strong triplet mechanism.     

Radical pair dynamics observed with pulse-mode product-yield-detected ESR

Three pulse sequences have been employed for laser and microwave-pulse irradiation in the pulse mode product-yield-detected ESR technique to detect the dynamical feature of transient radical pair. In this method, the decrease in spin adduct yield as functions of delay times for irradiation/termination of the microwave pulse after the laser pulse are simulated with the Runge-Kutta method for a detailed reaction model to obtain the rate constants of cage product formation, escape of the radical pair, as well as the hydrogen abstraction reaction. As the representative reaction systems, photoreduction of anthraquinone, anthraquinone-2-sulfonate, and benzophenone in SDS micellar solution were employed. Effects of cyclohexene, added as a hydrogen donor, NaCl and Ethanol, added to change the microviscosity of micelle, on these reaction rate constants have been tested.     

Pulsed 95 GHz high-field EPR heterodyne spectrometer with high spectral and time resolution

Various time resolved EPR methods are applied to different test samples to demonstrate the abilities of pulsed high-field EPR spectroscopy. Two-pulse-echo field swept EPR spectroscopy on a nitroxide radical shows the increased spectral resolution by separating different spin systems by their relaxation properties. Additionally N¹⁴ electron-spin-echo-envelope-modulation (ESEEM) is observed for these systems at fields as high as 3.5 T. Thus, the N¹⁴ hyperfine interaction couplings can be probed by ESEEM and pulsed ENDOR (electron-nuclear-double-resonance) experiments. The sensitivity of pulsed ENDOR experiments is compared with cw-ENDOR. The different linewidths and amplitudes of the two methods are discussed. Transient nutation experiments on light induced triplet states demonstrate the high sensitivity and time resolution of high-field pulsed EPR. The sensitivity and time resolution of our 95 GHz spectrometer are determined and compared with pulsed X-band EPR spectrometer performances.     

Theoretical treatment of volume localized NMR spectroscopy in weakly coupled spin systems

A pulse sequence is proposed for obtaining volume selective echoes with both chemical shift and homonuclear scalar coupling refocused. Theory, in terms of product operator formalism, is presented and the full response of the spin system is computed. The theoretical spatial dependence of the power signal given by spins localized in different planes (x=0,y=0, respectivez=0) is presented.     

Test studies of some conventional CW EPR spectrometer settings

The results obtained on the examination of different instrumental parameter settings as well as the influence of the accuracy of sample positioning on the EPR parameters for two types of EPR spectrometers — Bruker ER 200D SRC and a portable PS 100.X — are reported. The results obtained show good agreement between the EPR signal parameters and relative values of the spectrometer settings. The reproducibility of the results on re-inserting of one and the same sample in the cavity was evaluated with and without a holder fixed in the cavity.     

Structure of the product of intracomplex alkylation of target octanucleotide pd[TGTTTGGC] by means of 4-[N-methyl-N-(2-chloro-ethyl)-amino]benzyl-5′-phosphamido derivative of heptanucleotide pd[CCAAACA]: Two-dimensional1H-NMR spectroscopy and restrained molecular mechanics refinement

The spatial structure of a covalent adduct — the product of intracomplex alkylation at N-3-position of dC-8 nucleoside residue of target octanucleotide pd[TGTTTGGC] by means of 4-[N-methyl-N-(2-chloroethyl)amino]benzyl-5′-phosphamido derivative of heptanucleotide pd[CCAAACA] — has been investigated in aqueous solution by two-dimensional (2D)¹H-NMR spectroscopy and restrained molecular mechanics calculations. By using COSY, COSY-DQF and NOESY experiments the assignment of oligonucleotide protons as well as protons of modifying group was carried out. The correlation times of benzylamide fragment protons and those of neighbouring nucleotide residues dC-1 and dC-8 were shown to be equal and shorter thanτ _c of intraduplex nucleotides. The analysis of proton-proton coupling constants for H1′, H2′a, H2′b and H3′ protons showed all sugar residues to be in 2′-endo conformation. The distances between protons closed in the space were determined by means of a set of one-dimensional (1D) NOE experiments. The experimental distances were used as the constraints for energy minimization by molecular mechanics calculations. Eight conformations of benzylamide fragment of the covalent adduct differed with orientations of 4-N-methyl residue of the alkylating group and 1-methyleneamide linker function were constructed as starting structures in energy minimization procedure. Among of the resulting optimized structures only one S(Alk)8^* was found to satisfy both experimental data and energetic criteria. The benzylamide fragment in conformation S(Alk)8^* has been shown to localize in the region of lacked nucleoside residue of the duplex at the end of heptanucleotide chain less than 5 Å apart from the residues dC-1 and alkylated dC-8.     

Mono and bidimensional1H NMR and inverse detected13C NMR of the duplex d(CA)3·d(TG)3

The unambiguous assignment of the aromatic protons of the duplex d(CA)₃·d(TG)₃ was carried out with the aid of HMQC and HMBC inverse detected¹³C NMR experiments atT=278 K. The NOE connections of these protons with the imino protons of the complementary bases — established by 2D NOESY experiments — indicated that the duplex is characterized by a canonical Watson-Crick basepairing pattern. Monodimensional¹H NMR experiments, also carried out atT=278K, in the presence of varying amounts of NaCl and with water suppression by presaturation and by spin echo techniques, showed that the imino protons of the TA and CG pairs of the duplex exchange with water through a process of local base pair opening and with different exchange rates.     

Quantitative EPR spectrometry — “State of the art”

The purpose of the present review is to collect some results available in the literature in order to focus the attention of the world EPR community and thus to stimulate their activity on solving the problems of quantitative EPR spectrometry.     

IBM XT/AT data acquisition and processing system for Bruker ER 200D-SRC and ER 420 electron paramagnetic resonance spectrometers

Module giving IBM PC format of the EPR spectra recorded by Bruker ER 420 and ER 200D-SRC spectrometers is described. The files thus stored may be used for post-acquisition spectral processing using any program for this purpose and any IBM compatible PC.