Saturation Recovery Electron Paramagnetic Resonance Research Articles

Long-Range Electronic Couplings Observed in DNA By SR-EPR

DNA can self-assemble into a wide variety of pre-programmed 2-dimensional and 3-dimensional structures. This property, combined with the ability to conduct charge, makes DNA an attractive material for the fabrication of nanoscale circuitry, sensors, and catalysts. Fermi's Golden Rule, an equation governing the rate of charge transfer, describes the ease with which DNA conducts electrons or “holes” (positive charges). However, the predictive power of Fermi's Golden Rule is limited by the difficulty of independently measuring the terms that appear in this equation. One of these terms, the square of the electronic coupling matrix element, is proportional to the scalar exchange coupling between the charge donor and acceptor. Using a nitroxide radical and the paramagnetic Dy(III) ion as surrogates for donor and acceptor, we have measured scalar exchange couplings and their distance dependence in a family of DNA duplexes via saturation-recovery electron paramagnetic resonance (SR-EPR). Scalar exchange couplings are observed at distances as great as 5.6 nm. The decay in the scalar exchange coupling parallels the decay in electron transfer rates recently measured in DNA. The SR-EPR methodology is general and provides a new tool for determining the electronic coupling matrix element in Fermi's Golden Rule. The knowledge gained from these measurements may prove useful in designing DNA-based electronic devices.

Resolving Conformational and Rotameric Exchange in Spin-Labeled Proteins Using Saturation Recovery EPR

The function of many proteins involves equilibria between conformational substates, and to elucidate mechanisms of function it is essential to have experimental tools to detect the presence of conformational substates and to determine the time scale of exchange between them. Site-directed spin labeling (SDSL) has the potential to serve this purpose. In proteins containing a nitroxide side chain (R1), multicomponent electron paramagnetic resonance (EPR) spectra can arise either from equilibria involving different conformational substates or rotamers of R1. To employ SDSL to uniquely identify conformational equilibria, it is thus essential to distinguish between these origins of multicomponent spectra. Here we show that this is possible based on the time scale for exchange of the nitroxide between distinct environments that give rise to multicomponent EPR spectra; rotamer exchange for R1 lies in the ≈0.1-1 μs range, while conformational exchange is at least an order of magnitude slower. The time scales of exchange events are determined by saturation recovery EPR, and in favorable cases, the exchange rate constants between substates with lifetimes of approximately 1-70 μs can be estimated by the approach.

Structure and dynamics of a DNA-based model system for the study of electron spin–spin interactions

We report on the structure and dynamics of a model system for measuring long-range distances in biological macromolecules by saturation-recovery EPR. Four DNA duplexes that incorporate a paramagnetic dysprosium ion (Dy(III)) and a nitroxide spin-label were examined by electron paramagnetic resonance (EPR), circular dichroism (CD), and ultra-violet absorbance (UV) spectroscopy. Dy(III) is chelated by the modified base deoxythymidine-EDTA, (dT-EDTA). Electron spin-spin interactions between the Dy(III) ion and the nitroxide radical are observed at distances as great as approximately 5.3 nm. A slight change in the conformation of those nucleotides lying between the EDTA(Dy(III)) complex and the nitroxide spin-label results in a "stiffening" of the DNA helix on the EPR time scale. Changes in conformation and helix dynamics are due to the binding of the EDTA(Dy(III)) complex to the phosphodiester backbone of the complementary strand. Molecular mechanics calculations indicate that binding occurs in the 5' direction on the complementary strand, at a position 3 or 4 phosphates distant from the dT-EDTA(Dy(III))*dA base pair.

Measuring distances in proteins by saturation-recovery EPR

We describe a protocol for detecting electron spin-spin interactions between a radical and a metal ion in a protein or protein complex by saturation-recovery electron paramagnetic resonance (EPR). This protocol can be used with a protein containing an endogenous metal center and either an endogenous or synthetic radical species. We suggest a two-step approach whereby dipole-dipole or exchange interactions are first detected by continuous-wave EPR experiments and then quantified by saturation-recovery EPR. The latter measurements make it possible to measure long distances to within a few Angstroms. The protocol for making distance measurements by saturation-recovery EPR will take approximately 6 days to complete.

Progress towards a DNA-based model system for the study of electron spin–spin interactions

A DNA-based model system is described for studying electron spin–spin interactions between a paramagnetic metal ion and a nitroxide spin label. The modified base deoxythymidine-EDTA (dT-EDTA) chelates the divalent or trivalent metal ion and produces a new feature in the circular dichroism (CD) spectra that makes it possible to monitor local DNA melting. Based on the results of optical and electron paramagnetic resonance (EPR) experiments, we find that the terminus of the DNA duplex that incorporates dT-EDTA and the spin-label melts at a higher temperature than the rest of the DNA duplex. EPR microwave progressive power saturation experiments performed at 77 K are consistent with the specific binding of Dy(III) at the EDTA site and an intramolecular dipole–dipole interaction between the nitroxide spin-label and the chelated Dy(III). This model system should be suitable for studying the relaxation properties of metal ions by saturation-recovery EPR.

Accessibility and Dynamics of Nitroxide Side Chains in T4 Lysozyme Measured by Saturation Recovery EPR

Long pulse saturation recovery electron paramagnetic resonance spectroscopy is applied to the investigation of spin-labeled side chains placed along a regular helix extending from 128 to 135 in T4 lysozyme. Under an argon atmosphere, analysis of the exponential saturation recovery curves gives the spin-lattice relaxation rates of the nitroxides, which depend on the nitroxide side-chain dynamics. In the presence of the fast-relaxing paramagnetic reagents O 2 or NiEDDA, global analysis of the saturation recovery provides the spin-lattice relaxation rates as well as the Heisenberg exchange rates of the nitroxide with the reagents. As previously shown with power saturation methods, such exchange rates are direct measures of the solvent accessibility of the nitroxide side chains in the protein structure. The periodic dependence of the spin-lattice relaxation rates and the exchange rates along the 128–135 sequence reveal the presence of the helical structure, demonstrating the use of these parameters in structure determination. In general, multiple exponentials are required to fit the saturation recovery data, thus identifying multiple states of the side chain. In one case, multiple conformations detected in the spectrum are not evident in the saturation recovery, suggesting rapid exchange on the timescale of spin-lattice relaxation.

Explanation of Spin−Lattice Relaxation Rates of Spin Labels Obtained with Multifrequency Saturation Recovery EPR

Electron paramagnetic resonance (EPR) pulsed saturation recovery (pSR) measurements of spin-lattice relaxation rates have been made on nitroxide-containing fatty acids embedded in lipid bilayers by Hyde and co-workers. The data have been collected for a number of spin-labeled fatty acids at several microwave spectrometer frequencies (from 2 to 35 GHz). We compare these spin-lattice relaxation rates to those predicted by the Redfield theory incorporating several mechanisms. The dominant relaxation mechanism at low spectrometer frequencies is the electron-nuclear dipolar (END) process, with spin rotation (SR), chemical shift anisotropy (CSA), and a generalized spin diffusion (GSD) mechanism all contributing. The use of a wide range of spectrometer frequencies makes clear that the dynamics cannot be modeled adequately by rigid-body isotropic rotational motion. The dynamics of rigid-body anisotropic rotational motion is sufficient to explain the experimental relaxation rates within the experimental error. More refined models of the motion could have been considered, and our analysis does not rule them out. However, the results demonstrate that measurements at only two suitably chosen spectrometer frequencies are sufficient to distinguish anisotropic from isotropic motion. The results presented demonstrate that the principal mechanisms responsible for anisotropically driven spin-lattice relaxation are well understood in the liquids regime.

Pulse EPR Detection of Lipid Exchange between Protein-Rich Raft and Bulk Domains in the Membrane: Methodology Development and Its Application to Studies of Influenza Viral Membrane

A pulse saturation-recovery electron paramagnetic resonance (EPR) method has been developed that allows estimation of the exchange rates of a spin-labeled lipid between the bulk domain and the protein-rich membrane domain, in which the rate of collision between the spin label and molecular oxygen is reduced (slow-oxygen transport domain, or SLOT domain). It is based on the measurements of saturation-recovery signals of a lipid spin label as a function of concentrations of both molecular oxygen and the spin label. Influenza viral membrane, one of the simplest paradigms for the study of biomembranes, showed the presence of two membrane domains with slow and fast collision rates with oxygen (a 16-fold difference) at 30°C. The outbound rate from and the inbound rate into the SLOT domain (or possibly the rate of the domain disintegration and formation) were estimated to be 7.7 × 10 4 and 4.6 × 10 4 s −1, (15 μs residency time), respectively, indicating that the SLOT domain is highly dynamic and that the entire SLOT domain represents about one-third of the membrane area. Because the oxygen transport rate in the SLOT domain is a factor of two smaller than that in purple membrane, where bacteriorhodopsin is aggregated, we propose that the SLOT domain in the viral membrane is the cholesterol-rich raft domain stabilized by the trimers of hemagglutinin and/or the tetramers of neuraminidase.

Oriented Self-Association of Copper(II) Tetraphenylporphine in Liquid-Crystalline Lipid Bilayer Membranes: An EPR Study

Copper(II) tetraphenylporphine (CuTPP) has been found to partition favorably into dimyristoylphosphatidylcholine (DMPC) bilayer membranes. Electron paramagnetic resonance (EPR) spectra of oriented liquid-crystalline DMPC membranes indicate that for a high (≈1/25) CuTPP/DMPC molar ratio CuTPP is oriented with the plane of the molecule parallel to the bilayer surface. This result is in clear contrast to our previous observation that at low (≤1/100) CuTPP/DMPC molar ratio the plane of the molecule is preferentially perpendicular to the membrane surface (Pasenkiewicz-Gierula, M.; Subczynski, W. K.; Antholine, W. E. J. Phys. Chem. 1997, 101, 5596−5606). Measurements of the collision rate between CuTPP and the nitroxide moiety of stearic acid spin labels located at different depths in the membrane using saturation-recovery EPR spectroscopy lead to the conclusion that the change of the CuTPP orientation at a high CuTPP/DMPC molar ratio is coupled with self-association by planar stacking of CuTPP molecules near t...

Bimodal loop-gap resonator

A bimodal loop-gap resonator for use in electron paramagnetic resonance (EPR) spectroscopy at S band is described. It consists of two identical one-loop–one-gap resonators in coaxial juxtaposition. In one mode, the currents in the two loops are parallel and in the other antiparallel. By introducing additional capacitors between the loops, the frequencies of the two modes can be made to coincide. Details are given concerning variable coupling to each mode, tuning of the resonant frequency of one mode to that of the other, and adjustment of the isolation between modes. An equivalent circuit is given and network analysis carried out both experimentally and theoretically. EPR applications are described including (a) probing of the field distributions with DPPH, (b) continuous wave (cw) EPR with a spin-label line sample, (c) cw electron–electron double resonance (ELDOR), (d) modulation of saturation, and (e) saturation-recovery (SR) EPR. Bloch induction experiments can be performed when the sample extends half way through the structure, but microwave signals induced by Mx and My components of magnetization cancel when it extends completely through. This latter situation is particularly favorable for SR, modulation of saturation, and ELDOR experiments, which depend on observing Mz indirectly using a second weak observing microwave source.

Electron-electron spin-spin interaction in spin-labeled low-spin methemoglobin

Nitroxyl free radical electron spin relaxation times for spin-labeled low-spin methemoglobins were measured between 6 and 120 K by two-pulse electron spin echo spectroscopy and by saturation recovery electron paramagnetic resonance (EPR). Spin-lattice relaxation times for cyano-methemoglobin and imidazole-methemoglobin were measured between 8 and 25 K by saturation recovery and between 4.2 and 20 K by electron spin echo. At low temperature the iron electron spin relaxation rates are slow relative to the iron-nitroxyl electron-electron spin-spin splitting. As temperature is increased, the relaxation rates for the Fe(III) become comparable to and then greater than the spin-spin splitting, which collapses the splitting in the continuous wave EPR spectra and causes an increase and then a decrease in the nitroxyl electron spin echo decay rate. Throughout the temperature range examined, interaction with the Fe(III) increases the spin lattice relaxation rate (1/T1) for the nitroxyl. The measured relaxation times for the Fe(III) were used to analyze the temperature-dependent changes in the spin echo decays and in the saturation recovery (T1) data for the interacting nitroxyl and to determine the interspin distance, r. The values of r for three spin-labeled methemoglobins were between 15 and 15.5 A, with good agreement between values obtained by electron spin echo and saturation recovery. Analysis of the nitroxyl spin echo and saturation recovery data also provides values of the iron relaxation rates at temperatures where the iron relaxation rates are too fast to measure directly by saturation recovery or electron spin echo spectroscopy. These results demonstrate the power of using time-domain EPR measurements to probe the distance between a slowly relaxing spin and a relatively rapidly relaxing metal in a protein.

Electrochemical Generation and Electron Paramagnetic Resonance Studies of C60-, C602-, and C603-

The -1, -2, and -3 anions of C[sub 60] were generated electrochemically in 4:1 toluene-acetonitrile. The visible/near-IR spectra were monitored in situ. Square wave voltammograms and electronic spectra showed that after bulk electrolysis to produce the anions, the following percentages of the starting C[sub 60] concentration could be reoxidized to neutral C[sub 60] in typical data sets: -1 anion, 75%; -2 anion, 66%; -3 anion, 46%. Continuous wave (CW) electron paramagnetic resonance (EPR) spectra of the -1 and -3 anions exhibited broad signals that were temperature dependent. The averaging of anisotropy of the signals between 15 and 60 K is attributed to dynamic Jahn-Teller distortion. Electron spin-echo and saturation recovery EPR data for the -1 anion at 10 and 16 K showed that the electron spin relaxation rates are dependent upon position in the spectrum, which is attributed to variations in the Jahn-Teller distortion. For both the -1 and -3 anion above about 70 K the CW line shape of the EPR signal is electron spin-lattice relaxation rate determined. The EPR data indicate that the -2 anion is diamagnetic. 53 refs., 14 figs.

Mapping of collision frequencies for stearic acid spin labels by saturation-recovery electron paramagnetic resonance

Short pulse saturation-recovery electron paramagnetic resonance methods have been used to measure interactions of 14N:15N stearic acid spin label pairs in multilamellar liposomal dispersions composed of dimyristoyl-phosphatidylcholine (DMPC) and dielaidoylphosphatidylcholine (DEPC). Pairs consisting of various combinations of [14N]-16-, [14N]-12- or [14N]-5-doxylstearate, and [15N]-16-, [15N]-12-, or [15N]-5-doxylstearate were studied. SR experiments were performed at 27 degrees and 37 degrees C, and recovery signals were analyzed for initial conditions and multiexponential time constants by computer fitting using a damped least-squares approach. The time constants contain combinations of the electron spin lattice relaxation time, Tle, for each member of the spin-label pair, and the Heisenberg exchange rate constant, Kx. Spin-lattice relaxation times for each of the 14N and 15N stearic acid spin labels were determined, and it is noted that Tle for a given 15N-SASL was always slightly greater than that of the corresponding 14N-SASL. From Kx the bimolecular collision frequency was calculated, providing a detailed picture of molecular interactions. For both lipid systems the bimolecular collision rates were ordered as 12:5 less than 16:5 less than 5:5 less than 16:12 less than 12:12 less than 16:16. For all spin-label pairs studied, interaction frequencies were greater in DMPC than in DEPC. For the 16:16, 12:12, and 16:12 pairs, Kx was approximately 30% greater in DMPC than in DEPC, a significantly greater difference than is observed by conventional EPR methods. Further confirmation of the existence of vertical fluctuation of nitroxide moieties that are at the 16- (or 12) position toward the polar surfaces was obtained, with the frequency of 16:5 (or 12:5) interactions ~40% of the 16:16 (or 12:12) interaction frequency. In both DMPC and DEPC, Kx for homogeneous pairs increases as the doxyl moiety is moved further down the alkyl chain (i.e.,5:5 < 12:12 < 16:16), suggesting that steric effects or the local rotational mobility of the nitroxide group influence the frequency at which spin exchange occurs.

Conformation of spin-labeled melittin at membrane surfaces investigated by pulse saturation recovery and continuous wave power saturation electron paramagnetic resonance

Melittin spin-labeled specifically with a nitroxide at positions 7, 21, 23, or the amino terminus was bound to phospholipid membranes, and the exposure of the spin label to the aqueous phase was investigated by measurement of Heisenberg exchange with chromium oxalate in the solution. The exchange frequency was determined by saturation recovery electron paramagnetic resonance (EPR) using a loop-gap resonator. This method allows use of very low concentrations (less than 1 mM) of chromium oxalate compared with conventional measurements of EPR line broadening (typically 50 mM), thus avoiding problems associated with high metal ion concentration. Differences in exchange frequency between the various positions were also estimated by continuous wave power saturation methods. In either approach, the spin label at lysine 7 was found to be the most exposed to chromium oxalate whereas that at lysine 23 was found to be the least exposed. This is consistent with a model for the membrane bound peptide in which an amphiphilic helix lies with its axis parallel to the bilayer surface and the hydrophobic moment points toward the bilayer interior.

Direct detection of very slow two-jump processes by saturation recovery electron paramagnetic resonance spectroscopy

A theory of saturation recovery EPR has been developed to explore the very slow motional regime using the two-jump model. The EPR signal is predicted to be a biexponential curve for this motional model. From the two exponential decay constants λ1 and λ2 the exchange rate constant k can be calculated by the simple formula: k= 1/2 (λ2−λ1). Experimental results obtained from slowly tumbling 15N-TEMPOL in sec-butylbenzene have been fitted to the two-jump model. Even though this is a crude attempt, good agreement has been observed between the two-jump rate constant (k=0.043 μs−1) and the isotropic Brownian diffusion constant calculated from the hydrodynamic Debye expression (D=0.051 μs−1).

Interactions of 14N:15N stearic acid spin-label pairs: effects of host lipid alkyl chain length and unsaturation.

Electron-electron double resonance (ELDOR) and saturation recovery electron paramagnetic resonance (EPR) spectroscopy have been employed to examine the interactions of 14N:15N stearic acid spin-label pairs in fluid-phase model membrane bilayers composed of a variety of phospholipids. The [14N]-16-doxylstearate:[15N]-16-doxylstearate (16:16) pair was utilized to measure lateral diffusion of the spin-labels, while the [14N]-16-doxylstearate:[15N]-5-doxylstearate (16:5) pair provided information on vertical fluctuations of the 16-doxylstearate nitroxide moiety toward the membrane surface. Three saturated host lipids of varying alkyl chain length [dimyristoylphosphatidylcholine (DMPC), dipalmitoylphosphatidylcholine (DPPC), and distearoylphosphatidylcholine (DSPC)], an alpha-saturated, beta-unsaturated lipid [1-palmitoyl-2-oleoylphosphatidylcholine (POPC)], and phosphatidylcholine from a natural source [egg yolk phosphatidylcholine (egg PC)] were utilized as host lipids. Lateral diffusion of the stearic acid spin-labels was only slightly affected by alkyl chain length at a given reduced temperature (Tr) in the saturated host lipids but was significantly decreased in POPC at the same Tr. Lateral diffusion in DMPC, POPC, and egg PC was quite similar at 37 degrees C. A strong correlation was noted between lateral diffusion constants and rotational mobility of [14N]-16-doxylstearate. Vertical fluctuations were likewise only slightly influenced by alkyl chain length but were strongly diminished in POPC and egg PC relative to the saturated systems. This diminution of the 16:5 interaction was observed even under conditions where no differences were discernible by conventional EPR. These studies indicate that vertical fluctuation of 16-doxylstearate is quite sensitive to host lipid unsaturation and that ELDOR studies of interactions between 14N:15N spin-label pairs can provide information on spin-label motion beyond that given by conventional EPR.

Measurement of rotational molecular motion by time-resolved saturation transfer electron paramagnetic resonance

We have used saturation-recovery electron paramagnetic resonance (SR-EPR), a time-resolved saturation transfer EPR technique, to measure directly the microsecond rotational diffusion of spin-labeled proteins. SR-EPR uses an intense microwave pulse to saturate a spin population having narrow distribution of orientations with respect to the magnetic field. The time evolution of the signal is then observed. The signal increases in time as saturation is relieved by spin-lattice relaxation (Tl) as well as by saturation transfer due to spectral diffusion (Tsd), which is a function of rotational diffusion (Tr) and spectral position. In the presence of both events, the recovery is biphasic, with the initial phase related to both Tr and Tl, and the second phase determined only by Tl. We have measured the saturation recoveries of spin-labeled hemoglobin tumbling in media of known viscosities as a function of rotational correlation time (Tr) and pulse duration (tp). The Tr values estimated from the initial phase of recovery were in good agreement with theory. Variation of the pulse time can also be used to determine Tr. For tp less than Tsd, the recoveries were observed to be biphasic, for tp greater than Tsd a single-exponential. T1 values were determined from the recoveries after pulses quenching spectral diffusion or from the second phase of recovery after shorter pulses. These results demonstrate that SR-EPR is applicable to the study of motion of spin-labeled proteins. Its time resolution should provide a significant advantage over steady state techniques, particularly in the case of motional anisotropy or system heterogeneity.