Pulsed Dipolar EPR for Self-Limited Complexes of Oligonucleotides Studies.

Pulsed electron-electron double resonance (PELDOR) spectroscopy is a powerful method for determining nucleic acid (NA) structure and conformational dynamics. PELDOR with molecular dynamics (MD) simulations opens up unique possibilities for defining the conformational ensembles of flexible, three-dimensional, self-assembled complexes of NA. Understanding the diversity and structure of these complexes is vital for uncovering matrix and regulative biological processes in the human body and artificially influencing them for therapeutic purposes.

Hydrophilic Reduction-Resistant Spin Labels of Pyrrolidine and Pyrroline Series from 3,4-Bis-hydroxymethyl-2,2,5,5-tetraethylpyrrolidine-1-oxyl.

Highly resistant to reduction nitroxides open new opportunities for structural studies of biological macromolecules in their native environment inside living cells and for functional imaging of pH and thiols, enzymatic activity and redox status in living animals. 3,4-Disubstituted nitroxides of 2,2,5,5-tetraethylpyrrolidine and pyrroline series with a functional group for binding to biomolecules and a polar moiety for higher solubility in water and for more rigid attachment via additional coordination to polar sites were designed and synthesized. The EPR spectra, lipophilicities, kinetics of the reduction in ascorbate-containing systems and the decay rates in liver homogenates were measured.

Origin of Long-Range Hyperfine Couplings in the EPR Spectra of 2,2,5,5-Tetraethylpyrrolidine-1-oxyls.

Cyclic nitroxides with several bulky alkyl substituents adjacent to the nitroxide group are known to demonstrate a much higher stability to bioreduction than their tetramethyl analogues. Among these so-called "sterically shielded" nitroxides, the pyrrolidine derivatives are the most stable. The EPR spectra of some sterically shielded pyrrolidine-1-oxyls were reported to show one or two large additional doublet splittings with a hyperfine coupling (hfc) constant (ca.

Revealing light-induced structural shifts in G-quadruplex-porphyrin complexes: a pulsed dipolar EPR study.

The binding of G-quadruplex structures (G4s) with photosensitizers is of considerable importance in medicinal chemistry and drug discovery due to their promising potential in photodynamic therapy applications. G4s can experience structural changes as a result of ligand interactions and light exposure. Understanding these modifications is essential to uncover the fundamental biological roles of the complexes and optimize their therapeutic potential.

The Kinetic Solvent Effect on 1,3-Dipolar Cycloaddition of 2,2,5,5-Tetramethyl-3-imidazoline-3-oxide-1-oxyl.

The use of 2,2,5,5-tetramethyl-3-imidazoline-3-oxide-1-oxyl (1) as a controlling agent in Nitroxide Mediated Polymerization allows for activation of alkoxyamine homolysis by 1,3-dipolar cycloaddition of a vinyl monomer [Edeleva et al. Chem. Commun.

Effects of Spiro-Cyclohexane Substitution of Nitroxyl Biradicals on Dynamic Nuclear Polarization.

Spiro-substituted nitroxyl biradicals are widely used as reagents for dynamic nuclear polarization (DNP), which is especially important for biopolymer research. The main criterion for their applicability as polarizing agents is the value of the spin-spin exchange interaction parameter (), which can vary considerably when different couplers are employed that link the radical moieties. This paper describes a study on biradicals, with a ferrocene-1,1'-diyl-substituted 1,3-diazetidine-2,4-diimine coupler, that have never been used before as DNP agents.

Fullerene-based triplet spin labels: methodology aspects for pulsed dipolar EPR spectroscopy.

Triplet states of photoexcited organic molecules are promising spin labels with advanced spectroscopic properties for pulsed dipolar electron paramagnetic resonance (PD EPR) spectroscopy. Recently proposed triplet fullerene labels have shown great potential for double electron-electron resonance (DEER) distance measurements as "observer spins" due to a high quantum yield of the triplet state, hyperpolarization and relatively narrow EPR spectra. Here, we demonstrate the applicability of fullerene labels to other PD EPR techniques, such as relaxation induced dipolar modulation enhancement (RIDME) and laser induced magnetic dipolar spectroscopy (LaserIMD).

Immobilized Bisphosphonates as Potential Inhibitors of Bioprosthetic Calcification: Effects on Various Xenogeneic Cardiovascular Tissues.

Calcification is the major factor limiting the clinical use of bioprostheses. It may be prevented by the immobilization of bisphosphonic compounds (BPs) on the biomaterial. In this study, we assessed the accumulation and structure of calcium phosphate deposits in collagen-rich bovine pericardium (Pe) and elastin-rich porcine aortic wall (Ao) and bovine jugular vein wall (Ve) cross-linked with glutaraldehyde (GA) or diepoxy compound (DE).

Peek Inside the Water Mixtures of Ionic Liquids at Molecular Level: Microscopic Properties Probed by EPR Spectroscopy.

Many ionic liquids (ILs) can be mixed with water, forming either true solutions or emulsions. This favors their applications in many respects, but at the same time might strongly alter their physicochemical properties. A number of methods exist for studying the macroscopic properties of such mixtures, whereas understanding their characteristics at micro/nanoscale is rather challenging.

The effects of nitroxide structure upon H Overhauser dynamic nuclear polarization efficacy at ultralow-field.

The efficacy in H Overhauser dynamic nuclear polarization in liquids at ultralow magnetic field (ULF, B = 92 ± 0.8 µT) and polarization field (B = 1-10 mT) was studied for a broad variety of 26 different spin probes. Among others, piperidine, pyrrolidine, and pyrroline radicals specifically synthesized for this study, along with some well-established commercially available nitroxides, were investigated.

A Simple Method of Synthesis of 3-Carboxy-2,2,5,5-Tetraethylpyrrolidine-1-oxyl and Preparation of Reduction-Resistant Spin Labels and Probes of Pyrrolidine Series.

Stable free radicals are widely used as molecular probes and labels in various biophysical and biomedical research applications of magnetic resonance spectroscopy and imaging. Among these radicals, sterically shielded nitroxides of pyrrolidine series demonstrate the highest stability in biological systems. Here, we suggest new convenient procedure for preparation of 3-carboxy-2,2,5,5-tetraethylpyrrolidine-1-oxyl, a reduction-resistant analog of widely used carboxy-Proxyl, from cheap commercially available reagents with the yield exceeding the most optimistic literature data.

Treatment with bisphosphonates to mitigate calcification of elastin-containing bioprosthetic materials.

This study evaluated the ability of bisphosphonates (BPAs) of different molecular structures to mitigate the calcification of porcine aortic wall (PAW) and bovine jugular vein wall (BJVW). Tissues cross-linked with glutaraldehyde (GA) or diepoxide (DE) were modified with pamidronic acid (PAM), alendronic acid (ALE), neridronic acid (NER) (type 1 BPAs); 2-(2'-carboxyethylamino)ethylidene-1,1-bisphosphonic acid (CEABA), 2-(5-carboxypentylamino)ethylidene-1,1-bisphosphonic acid (CPABA) (type 2); and zoledronic acid (ZOL) (type 3). After implanting the tissue samples subcutaneously in 100 rats, calcification was examined using atomic absorption spectrophotometry (60-day explants) and light microscopy after von Kossa staining (10- and 30-day explants).

DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling.

A DNA molecule is under continuous influence of endogenous and exogenous damaging factors, which produce a variety of DNA lesions. Apurinic/apyrimidinic sites (abasic or AP sites) are among the most common DNA lesions. In this work, we applied pulse dipolar electron paramagnetic resonance (EPR) spectroscopy in combination with molecular dynamics (MD) simulations to investigate in-depth conformational changes in DNA containing an AP site and in a complex of this DNA with AP endonuclease 1 (APE1).

Triplet Fullerenes as Prospective Spin Labels for Nanoscale Distance Measurements by Pulsed Dipolar EPR Spectroscopy.

Precise nanoscale distance measurements by pulsed electron paramagnetic resonance (EPR) spectroscopy play a crucial role in structural studies of biomolecules. The properties of the spin labels used in this approach determine the sensitivity limits, attainable distances, and proximity to biological conditions. Herein, we propose and validate the use of photoexcited fullerenes as spin labels for pulsed dipolar (PD) EPR distance measurements.

In search of the best xenogeneic material for a paediatric conduit: an experimental study.

Objectives: The development of calcification-resistant bioprosthetic materials is a very important challenge for paediatric surgery. The subcutaneous implantation in rats is the well-known first-stage model for this kind of research. Using this model, we aimed to compare calcification of the porcine aortic wall and bovine pericardium and jugular vein wall cross-linked with glutaraldehyde (GA) and ethylene glycol diglycidyl ether (DE).

Electron Paramagnetic Resonance Measurements of Reactive Oxygen Species by Cyclic Hydroxylamine Spin Probes.

Significance: Oxidative stress contributes to numerous pathophysiological conditions such as development of cancer, neurodegenerative, and cardiovascular diseases. A variety of measurements of oxidative stress markers in biological systems have been developed; however, many of these methods are not specific, can produce artifacts, and do not directly detect the free radicals and reactive oxygen species (ROS) that cause oxidative stress. Electron paramagnetic resonance (EPR) is a unique tool that allows direct measurements of free radical species.

Room-temperature electron spin relaxation of nitroxides immobilized in trehalose: Effect of substituents adjacent to NO-group.

Trehalose has been recently promoted as efficient immobilizer of biomolecules for room-temperature EPR studies, including distance measurements between attached nitroxide spin labels. Generally, the structure of nitroxide influences the electron spin relaxation times, being crucial parameters for room-temperature pulse EPR measurements. Therefore, in this work we investigated a series of nitroxides with different substituents adjacent to NO-moiety including spirocyclohexane, spirocyclopentane, tetraethyl and tetramethyl groups.

A versatile approach for site-directed spin labeling and structural EPR studies of RNAs.

Site-directed spin labeling (SDSL) is widely applied for structural studies of biopolymers by electron paramagnetic resonance (EPR). However, SDSL of long RNA sequences still remains a challenging task. Here, we propose a novel SDSL approach potentially suitable for long natural RNAs, which is based on the attachment of a linker containing an aliphatic amino group to the target nucleotide residue followed by selective coupling of a spin label to this amino group.

Synthesis of 2,5-bis(spirocyclohexane)-substituted nitroxides of pyrroline and pyrrolidine series, including thiol-specific spin label: an analogue of MTSSL with long relaxation time.

The nitroxides of 7-azadispiro[5.1.5.

Deactivation of excited states of kynurenine covalently linked to nitroxides.

Due to ability of stable nitroxides to interact with free radicals, they are used as antioxidants for therapeutic and research goals in biology and medicine. A modern trend in medical chemistry is the design of multifunctional molecules such as UV absorbers covalently bound to nitroxides, which provides both UV protection and antioxidant properties combined in the same molecule. In the present work, we report the synthesis of conjugates of a natural UV filter kynurenine (KN) with nitroxides (KN-RNO(•) conjugates) and the study of their photochemical properties in aqueous and methanol solutions.