What are the methodological and theoretical prospects for paramagnetic NMR in structural biology? A glimpse into the crystal ball

NMR spectroscopy is very sensitive to the presence of unpaired electrons, which perturb the NMR chemical shifts, J splittings and nuclear relaxation rates. These paramagnetic effects have attracted increasing attention over the last decades, and their use is expected to increase further in the future because they can provide structural information not easily achievable with other techniques. In fact, paramagnetic data provide long range structural restraints that can be used to assess the accuracy of crystal structures in solution and to improve them by simultaneous refinements with the X-ray data. They are also precious for obtaining information on the conformational variability of biomolecular systems, possibly in conjunction with SAXS and/or DEER data. We foresee that new tools will be developed in the next years for the simultaneous analysis of the paramagnetic data with data obtained from different techniques, in order to take advantage synergistically of the information content of all of them. Of course, the use of the paramagnetic data for structural purposes requires the knowledge of the relationship between these data and the molecular coordinates. Recently, the equations commonly used, dating back to half a century ago, have been questioned by first principle quantum chemistry calculations. Our prediction is that further theoretical/computational improvements will essentially confirm the validity of the old semi-empirical equations for the analysis of the experimental paramagnetic data.

Pulse EPR in biological systems - Beyond the expert's courtyard

Application of EPR to biological systems includes many techniques and applications. In this short perspective, which dares to look into the future, I focus on pulse EPR, which is my field of expertise. Generally, pulse EPR techniques can be divided into two main groups: (1) hyperfine spectroscopy, which explores electron-nuclear interactions, and (2) pulse-dipolar (PD) EPR spectroscopy, which is based on electron-electron spin interactions. Here I focus on PD-EPR because it has a better chance of becoming a widely applied, easy-to-use table-top method to study the structural and dynamic aspects of bio-molecules. I will briefly introduce this technique, its current state of the art, the challenges it is facing, and finally I will describe futuristic scenarios of low-cost PD-EPR approaches that can cross the diffusion barrier from the core of experts to the bulk of the scientific community.

The world as viewed by and with unpaired electrons

Recent advances in electron paramagnetic resonance (EPR) include capabilities for applications to areas as diverse as archeology, beer shelf life, biological structure, dosimetry, in vivo imaging, molecular magnets, and quantum computing. Enabling technologies include multifrequency continuous wave, pulsed, and rapid scan EPR. Interpretation is enhanced by increasingly powerful computational models.

Fingernail dosimetry: current status and perspectives

A summary of recent developments in fingernail EPR dosimetry is presented in this paper. Until 2007, there had been a very limited number of studies of radiation-induced signals in fingernails. Although these studies showed some promising results, they were not complete with regard to the nature of non-radiation signals and the variability of dose dependence in fingernails. Recent study has shown that the two non-radiation components of the EPR spectrum of fingernails are originated from mechanical stress induced in the samples at their cut. The mechanical properties of fingernails were found to be very similar to those of a sponge; therefore, an effective way to eliminate their mechanical deformation is by soaking them in water. Stress caused by deformation can also significantly modify the dose response and radiation sensitivity. Consequently, it is critically important to take into account the mechanical stress in fingernail samples under EPR dose measurements. Obtained results have allowed formulating a prototype of a protocol for dose measurements in human fingernails.

Recent advances and applications of site-directed spin labeling

Site-directed spin labeling has become a popular biophysical tool for the characterization of protein structure, dynamics and conformational change. This method is well suited and widely used to study small soluble proteins, membrane proteins and large protein complexes. Recent advances in site-directed spin labeling methodology have occurred in two areas. The first involves an understanding of the conformations and local dynamics of the spin-labeled sidechain, including the features of proteins that influence electron paramagnetic resonance lineshape. The second advance is the application of pulse techniques to determine long-range distances and distance distributions in proteins. During the past two years, these technical developments have been used to address several important problems concerning the molecular function of proteins.

Joint International Conference on EPR Spectroscopy and wound healing

The International Conference on Electron Paramagnetic Resonance Spectroscopy and Imaging of Biological Systems (EPR 2005) was held September 4 through 9, 2005, at Columbus, Ohio, U.S.A. Nearly 200 participants from 16 countries presented recent advances on the use of EPR technology to study biologic processes, with an emphasis on human health. For the first time, the EPR conference allied with the Wound Healing Conference, and the alliance opened an avenue for successful amalgamation of the basic biomedical and clinical aspects of wound healing with EPR technology and vice versa. This should lead to emerging applications of EPR technology in biomedical research and clinical practice.

The Third International Intercomparison on EPR Tooth Dosimetry: part 2, final analysis

The objective of the Third International Intercomparison on EPR Tooth Dosimetry was to evaluate laboratories performing tooth enamel dosimetry <300 mGy. Final analysis of results included a correlation analysis between features of laboratory dose reconstruction protocols and dosimetry performance. Applicability of electron paramagnetic resonance (EPR) tooth dosimetry at low dose was shown at two applied dose levels of 79 and 176 mGy. Most (9 of 12) laboratories reported the dose to be within 50 mGy of the delivered dose of 79 mGy, and 10 of 12 laboratories reported the dose to be within 100 mGy of the delivered dose of 176 mGy. At the high-dose tested (704 mGy) agreement within 25% of the delivered dose was found in 10 laboratories. Features of EPR dose reconstruction protocols that affect dosimetry performance were found to be magnetic field modulation amplitude in EPR spectrum recording, EPR signal model in spectrum deconvolution and duration of latency period for tooth enamel samples after preparation.

ESR spectrometry: a future-oriented tool for dosimetry and dating

ESR spectroscopy is currently taking root as a key technology in dosimetry, dating and imaging. In dosimetry, it competes with cytometry in the fields of biological dosimetry and retrospective dosimetry, leads in high-level reference and routine dosimetry, is high-ranking among the methods to identify radiation preserved foods, represents a method of choice to date geological, archaeological and paleontological materials back millions of years, and has demonstrated capacity for imaging. Further scientific and technological progress as predicted in the recent past (Appl. Radiat. Isot. 52 (2000) 1023) is reviewed here. Additionally, the review is expanded to include international reports and recommendations on ESR dosimetry and dose reconstruction, under way at the American Society for Testing and Materials (ASTM), the International Organisation of Standards (ISO), the International Atomic Energy Agency (IAEA) and the International Commission on Radiation Units and Measurements (ICRU). Emphasis is placed on interpretation of tooth enamel doses in terms of organ and effective doses, using CT-based virtual humans. The future of EPR spectroscopy for in situ dose measurements is noted, depicting a non-destructive in vivo dosimetry applicable directly to individuals, but also to hominid and animal fossils for direct dating.

Functional imaging of intratumoral hypoxia

PURPOSE

Tumor hypoxia plays a fundamental role in tumor progression and treatment resistance. Recent evidence that hypoxia also influences the regulation and transcription of various genes involved in malignant growth and metastases, and promotes a more aggressive tumor phenotype makes its diagnosis even more important.

PROCEDURES

The evidence for the biology of hypoxia in tumors, and imaging of hypoxia with different technologies was reviewed through literature review and Medline searches, and clinical studies with 18F-fluoromisonidazole (FMISO) Positron Emission Tomography (PET).

RESULTS

Until recently, determination of the level of tumor oxygenation was only possible using invasive methods that limited its clinical application. Imaging techniques that have shown promise in assessing hypoxia include magnetic resonance imaging and spectroscopy, single photon emission computed tomography (SPECT) and PET. Quantitative hypoxia measurement with 18F-FMISO PET in patients with malignant gliomas and lung cancer have demonstrated intratumoural hypoxia and dissociation of glucose metabolism from hypoxia in some cases, indicating the complex nature of cellular metabolic response to stress.

CONCLUSION

The emerging role of therapies that have improved efficacy in hypoxic conditions, and recent advances in the ability to noninvasively measure in vivo intratumoral hypoxia with functional imaging has renewed interest in the clinical measurement of tumor hypoxia and its impact on cancer treatment.

Recent progress in in vivo ESR spectroscopy

The generation of free radicals and redox status is related to various diseases and injuries that are related to radiation, aging, ischemia-reperfusion, and other oxidative factors. In vivo electron spin resonance (ESR) spectroscopy is noninvasive and detects durable free radicals in live animals. ESR spectrometers for in vivo measurements operate at a lower frequency (approximately 3.5 GHz, approximately 1 GHz, 700 MHz, and approximately 300 MHz) than usual (9-10 GHz). Several types of resonators have been designed to minimize the dielectric loss of electromagnetic waves caused by water in animal bodies. In vivo ESR spectroscopy and its imaging have been used to analyze radical generation, redox status, partial pressure of oxygen and other conditions in various disease and injury models related to oxidative stress with probes, such as nitroxyl radicals. Through these applications, the clarification of the mechanisms related to oxidative diseases (injuries) and the accumulation of basic data for radiological cancer therapy are now ongoing. In vivo ESR measurement is performed in about 10 laboratories worldwide, including ours. To introduce in vivo ESR spectroscopy to life scientists, this article reviews the recent progress of in vivo ESR spectroscopy in instrumentation and its application to the life sciences.

In vivo EPR: when, how and why?

This special issue is aimed at providing the readers of this journal with an indication of the exciting and important areas in which in vivo electron paramagnetic resonance (EPR) [or equivalently electron spin resonance (ESR)] is making contributions to experimental progress and to provide perspectives on future developments, including the potential for in vivo EPR to be an important new clinical tool. There also are many situations where the combination of in vivo EPR with NMR may be very synergistic. EPR (ESR) is a magnetic resonance-based technique that detects species with unpaired electrons. The technique has become a major tool in diverse fields ranging from biology and chemistry to solid-state physics. In the last few years, many publications have demonstrated that EPR measurements in living animals (in vivo EPR) can provide very significant new insights to physiology, pathophysiology and pharmacology. The most successful applications of in vivo EPR have been non-invasive measurements of oxygen, nitric oxide, bioradicals, pH and redox state, with applications in oncology, cardiology, neuroscience and toxicology. EPR also appears to be the method of choice for measuring radiation dose retrospectively, including the potential to do this in vivo in human subjects. While far from comprehensive, the reviews, original contributions and viewpoints provided in this issue by several leaders in the field of in vivo EPR should provide the readers with confirmation that in vivo EPR is an exciting field that is likely to provide very valuable complementary information for many NMR-based studies in experimental animals and, probably, also for clinical studies.

Assessment of tumor oxygenation by electron paramagnetic resonance: principles and applications

This review paper attempts to provide an overview of the principles and techniques that are often termed electron paramagnetic resonance (EPR) oximetry. The paper discusses the potential of such methods and illustrates they have been successfully applied to measure oxygen tension, an essential parameter of the tumor microenvironment. To help the reader understand the motivation for carrying out these measurements, the importance of tumor hypoxia is first discussed: the basic issues of why a tumor is hypoxic, why these hypoxic microenvironments promote processes driving malignant progression and why hypoxia dramatically influences the response of tumors to cytotoxic treatments will be explained. The different methods that have been used to estimate the oxygenation in tumors will be reviewed. To introduce the basics of EPR oximetry, the specificity of in vivo EPR will be discussed by comparing this technique with NMR and MRI. The different types of paramagnetic oxygen sensors will be presented, as well as the methods for recording the information (EPR spectroscopy, EPR imaging, dynamic nuclear polarization). Several applications of EPR for characterizing tumor oxygenation will be illustrated, with a special emphasis on pharmacological interventions that modulate the tumor microenvironment. Finally, the challenges for transposing the method into the clinic will also be discussed.

Clinical applications of EPR: overview and perspectives

The development and use of in vivo techniques for strictly experimental applications in animals has been very successful, and these results now have made possible some very attractive potential clinical applications. The area with the most obvious immediate, effective and widespread clinical use is oximetry, where EPR almost uniquely can make repeated and accurate measurements of pO2 in tissues. Such measurements can provide clinicians with information that can impact directly on diagnosis and therapy, especially for oncology, peripheral vascular disease and wound healing. The other area of immediate and timely importance is the unique ability of in vivo EPR to measure clinically significant exposures to ionizing radiation 'after-the-fact', such as may occur due to accidents, terrorism or nuclear war. There are a number of other capabilities of in vivo EPR that also potentially could become extensively used in human subjects. In pharmacology the unique capabilities of in vivo EPR to detect and characterize free radicals could be applied to measure free radical intermediates from drugs and oxidative process. A closely related area of potential widespread applications is the use of EPR to measure nitric oxide. These often unique capabilities, combined with the sensitivity of EPR spectra to the immediate environment (e.g. pH, molecular motion, charge) have already resulted in some very productive applications in animals and these are likely to expand substantially in the near future. They should provide a continually developing base for extending clinical uses of in vivo EPR. The challenges for achieving full implementation include adapting the spectrometer for safe and comfortable measurements in human subjects, achieving sufficient sensitivity for measurements at the sites of the pathophysiological processes that are being measured, and establishing a consensus on the clinical value of the measurements.

Radio frequency continuous-wave and time-domain EPR imaging and Overhauser-enhanced magnetic resonance imaging of small animals: instrumental developments and comparison of relative merits for functional imaging

Electron paramagnetic resonance (EPR) imaging in the continuous wave (CW) and time-domain modes, as well as Overhauser-enhanced magnetic resonance imaging in vivo is described. The review is based mainly on the CW and time-domain EPR instrumentation at 300 MHz developed in our laboratory, and the relative merits of these methods for functional in vivo imaging of small animals to assess hypoxia and tissue redox status are described. Overhauser imaging of small animals at magnetic fields in the range 10-15 mT that is being carried out in our laboratory for tumor imaging and the evaluation of tumor hypoxia based on quantitative evaluation of Overhauser enhancement is also described. Alternate approaches to spectral-spatial imaging using the transverse decay constants to infer in situ line widths and hence in vivo pO2 using CW and time-domain EPR imaging are also discussed. The nature of the spin probes used, the quality of the images obtained in all the three methods, the achievable resolution, limitations and possible future directions in small animal functional imaging with these modalities are summarized.

Tissue oxygenation in sepsis; new insights from in vivo EPR

Nitric oxide (NO) is a key mediator in the maldistribution of oxygen by tissue and organ dysfunction observed in sepsis. Despite this, few techniques are capable of measuring these parameters directly in vivo. We describe here several techniques that have been developed by our group to address this directly by in vivo EPR in animal models of sepsis. Oxygen-sensitive materials can be implanted or administered and report on local tissue pO2. Spin trapping of NO can simultaneously report on tissue NO content. Repeat measures of these parameters can be made directly from a defined tissue site, allowing development of new models and experiments to study the defects in tissue and organ function seen in sepsis.

[Progress and application of free radical determination techniques in the biological domain]

Seeking for convenient, rapid and highly effective techniques of free radical determination is a key point for studying the biologic mechanism of free radicals. This paper reviewed the progress of these techniques in biological domain and described the electron spin resonance imaging [correction of imagine] (ESRI) technique development since the 1990s.

[The development of nanoparticles on DNA isolation and purification]

Magnetic nanoparticle is a new solid-support of affinity chromatography. The particle size is small and it has super-paramagnetism. It has large surface area and it can be endowed many reaction groups such as streptavidin, antibody or DNA fragments. The target DNA can be separated in magnetic field. The magnetic nanoparticle is applied in the biomolecular field gradually and it has a very broad prospect of appliance.

ESR dating: is it still an 'experimental' technique?

Nearly 25 years ago, Motoji Ikeya demonstrated the potential of ESR dating. From a single substance (stalagmitic carbonate) and a single site (Akiyoshi Cavern), the field has grown to include materials from all over the world and time periods from a few thousand years ago to several million years ago. A vigorous program of instrumentation development has increased the precision of measurements as well as opening up new ways of collecting and interpreting spectra. Yet there are still references to ESR dating as an 'experimental' technique, one which cannot be trusted to produce dates that are accurate or precise. This paper discusses areas for which this is true and suggests what should be done to convince skeptics. Other areas for which the evidence suggests that ESR is at least as reliable as 'standard' methods will also be covered.

From dating to biophysics--20 years of progress in applied ESR spectroscopy

ESR spectroscopy represents a tool for quantitative radiation analysis that was developed somehow simultaneously for dating purposes in Japan and in Germany for high-level standardization, in the mid-seventies. Meanwhile, ESR dosimetry has reached an established metrology level. Present research fields of ESR dosimetry consider post-accident dose reconstruction in the environment, and biophysical dosimetry using human tissues. The latter promises a re-definition of radiation risk for chronicle exposure to be derived from individuals of the early nuclear facilities in Russia, and hopefully United States in the future. An attempt is made to sketch development and potential future of the ESR technique.