Alexey S. Kiryutin

Transfer of CIDNP among coupled spins at low magnetic field

Coherent polarization transfer among groups of dynamically polarized spins is explored and applied to field cycling experiments where spin evolution proceeds at low magnetic field while observation is performed at high field. The case of two nonequivalent spins-1/2 with scalar spin coupling is considered theoretically in detail for the cases of sudden and adiabatic field change. The criterion for efficient polarization transfer is derived theoretically and consistently confirmed experimentally for three photochemical reactions, involving spin systems of increasing complexity that exhibit chemically induced dynamic nuclear polarization: (1) the two polarized protons of the purine base of adenosine monophosphate; (2) four coupled indole protons of tryptophan; and (3) long-range polarization transfer among the aliphatic protons of cycloundecanone. The importance of polarization transfer in other cases with non-equilibrium population of the nuclear spin levels and the possibility of its utilization in field cycling NMR studies are discussed.

Manipulating spin hyper-polarization by means of adiabatic switching of a spin-locking RF-field

We propose a technique for transferring the multiplet spin polarization (CIDNP or PHIP, or one created by any other method), which is the mutual entanglement of spins, into net hyper-polarization with respect to the direction of a high magnetic field by slowly (adiabatically) switching-off a strong external RF-field with a specially selected frequency. The net hyper-polarized molecules can then be used in NMR spectroscopy or imaging for strong signal enhancement.

Long-lived spin states as a source of contrast in magnetic resonance spectroscopy and imaging.

A method is proposed to create Long-Lived spin States (LLSs) from longitudinal spin magnetization, which is based on adiabatic switching of a Radio-Frequency (RF) field with proper frequency. The technique is simple to implement with standard Nuclear Magnetic Resonance (NMR) equipment, providing an excellent conversion of population from the triplet T+ (or T-) state to the singlet state of a pair of spins and back. The method has been tested for the amino acid tyrosine and its partially deuterated isotopomer; for the deuterated compound, we have achieved a LLS lifetime, which exceeds the longitudinal relaxation time by a factor of 21. Furthermore, by slightly modifying the method, an enhanced contrast with respect to LLSs in NMR spectra is achieved; contrast enhancements of more than 1200 are feasible. This enables efficient suppression of longitudinal spin magnetization in NMR allowing one to look selectively at LLSs. Using this method we have demonstrated that not only spectral but also spatial contrast can be achieved: we have obtained spatial NMR images with strongly improved contrast originating from the difference of LLS lifetimes at different positions in the sample.

Exploiting adiabatically switched RF-field for manipulating spin hyperpolarization induced by parahydrogen

A method for precise manipulation of non-thermal nuclear spin polarization by switching a RF-field is presented. The method harnesses adiabatic correlation of spin states in the rotating frame. A detailed theory behind the technique is outlined; examples of two-spin and three-spin systems prepared in a non-equilibrium state by Para-Hydrogen Induced Polarization (PHIP) are considered. We demonstrate that the method is suitable for converting the initial multiplet polarization of spins into net polarization: compensation of positive and negative lines in nuclear magnetic resonance spectra, which is detrimental when the spectral resolution is low, is avoided. Such a conversion is performed for real two-spin and three-spin systems polarized by means of PHIP. Potential applications of the presented technique are discussed for manipulating PHIP and its recent modification termed signal amplification by reversible exchange as well as for preparing and observing long-lived spin states.

Complete magnetic field dependence of SABRE-derived polarization

Signal amplification by reversible exchange (SABRE) is a promising hyperpolarization technique, which makes use of spin‐order transfer from parahydrogen (the H2 molecule in its singlet spin state) to a to‐be‐polarized substrate in a transient organometallic complex, termed the SABRE complex. In this work, we present an experimental method for measuring the magnetic field dependence of the SABRE effect over an ultrawide field range, namely, from 10 nT to 10 T. This approach gives a way to determine the complete magnetic field dependence of SABRE‐derived polarization. Here, we focus on SABRE polarization of spin‐1/2 hetero‐nuclei, such as 13C and 15N and measure their polarization in the entire accessible field range; experimental studies are supported by calculations of polarization. Features of the field dependence of polarization can be attributed to level anticrossings in the spin system of the SABRE complex. Features at magnetic fields of the order of 100 nT–1 μT correspond to “strong coupling” of protons and hetero‐nuclei, whereas features found in the mT field range stem from “strong coupling” of the proton system. Our approach gives a way to measuring and analyzing the complete SABRE field dependence, to probing NMR parameters of SABRE complexes and to optimizing the polarization value.

A highly versatile automatized setup for quantitative measurements of PHIP enhancements

The design and application of a versatile and inexpensive experimental extension to NMR spectrometers is described that allows to carry out highly reproducible PHIP experiments directly in the NMR sample tube, i.e. under PASADENA condition, followed by the detection of the NMR spectra of hyperpolarized products with high spectral resolution. Employing this high resolution it is feasible to study kinetic processes in the solution with high accuracy. As a practical example the dissolution of hydrogen gas in the liquid and the PHIP kinetics during the hydrogenation reaction of Fmoc-O-propargyl-l-tyrosine in acetone-d6 are monitored. The timing of the setup is fully controlled by the pulse-programmer of the NMR spectrometer. By flushing with an inert gas it is possible to efficiently quench the hydrogenation reaction in a controlled fashion and to detect the relaxation of hyperpolarization without a background reaction. The proposed design makes it possible to carry out PHIP experiments in an automatic mode and reliably determine the enhancement of polarized signals.

8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme

8-oxoguanine is one of the most abundant and impactful oxidative DNA lesions. However, the reasons underlying its effects, especially those not directly explained by the altered base pairing ability, are poorly understood. We report the effect of the lesion on the action of EcoRI, a widely used restriction endonuclease. Introduction of 8-oxoguanine inside, or adjacent to, the GAATTC recognition site embedded within the Drew—Dickerson dodecamer sequence notably reduced the EcoRI activity. Solution NMR revealed that 8-oxoguanine in the DNA duplex causes substantial alterations in the sugar—phosphate backbone conformation, inducing a BI→BII transition. Moreover, molecular dynamics of the complex suggested that 8-oxoguanine, although does not disrupt the sequence-specific contacts formed by the enzyme with DNA, shifts the distribution of BI/BII backbone conformers. Based on our data, we propose that the disruption of enzymatic cleavage can be linked with the altered backbone conformation and dynamics in the free oxidized DNA substrate and, possibly, at the protein—DNA interface.

Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation

Abstract DNA damage can affect various regulatory elements of the genome, with the consequences for DNA structure, dynamics, and interaction with proteins remaining largely unexplored. We used solution NMR spectroscopy, restrained and free molecular dynamics to obtain the structures and investigate dominant motions for a set of DNA duplexes containing CpG sites permuted with combinations of 5-methylcytosine (mC), the primary epigenetic base, and 8-oxoguanine (oxoG), an abundant DNA lesion. Guanine oxidation significantly changed the motion in both hemimethylated and fully methylated DNA, increased base pair breathing, induced BI→BII transition in the backbone 3′ to the oxoG and reduced the variability of shift and tilt helical parameters. UV melting experiments corroborated the NMR and molecular dynamics results, showing significant destabilization of all methylated contexts by oxoG. Notably, some dynamic and thermodynamic effects were not additive in the fully methylated oxidized CpG, indicating that the introduced modifications interact with each other. Finally, we show that the presence of oxoG biases the recognition of methylated CpG dinucleotides by ROS1, a plant enzyme involved in epigenetic DNA demethylation, in favor of the oxidized DNA strand. Thus, the conformational and dynamic effects of spurious DNA oxidation in the regulatory CpG dinucleotide can have far-reaching biological consequences.

Using optimal control methods with constraints to generate singlet states in NMR

A method is proposed for optimizing the performance of the APSOC (Adiabatic-Passage Spin Order Conversion) technique, which can be exploited in NMR experiments with singlet spin states. In this technique magnetization-to-singlet conversion (and singlet-to-magnetization conversion) is performed by using adiabatically ramped RF-fields. Optimization utilizes the GRAPE (Gradient Ascent Pulse Engineering) approach, in which for a fixed search area we assume monotonicity to the envelope of the RF-field. Such an approach allows one to achieve much better performance for APSOC; consequently, the efficiency of magnetization-to-singlet conversion is greatly improved as compared to simple model RF-ramps, e.g., linear ramps. We also demonstrate that the optimization method is reasonably robust to possible inaccuracies in determining NMR parameters of the spin system under study and also in setting the RF-field parameters. The present approach can be exploited in other NMR and EPR applications using adiabatic switching of spin Hamiltonians.

cis Versus trans-Azobenzene: Precise Determination of NMR Parameters and Analysis of Long-Lived States of 15N Spin Pairs

We provide a detailed evaluation of nuclear magnetic resonance (NMR) parameters of the cis- and trans-isomers of azobenzene (AB). For determining the NMR parameters, such as proton–proton and proton–nitrogen J-couplings and chemical shifts, we compared NMR spectra of three different isotopomers of AB: the doubly 15N labeled azobenzene, 15N,15N′-AB, and two partially deuterated AB isotopomers with a single 15N atom. For the total lineshape analysis of NMR spectra, we used the recently developed ANATOLIA software package. The determined NMR parameters allowed us to optimize experiments for investigating singlet long-lived spin states (LLSs) of 15N spin pairs and to measure LLS lifetimes in cis-AB and trans-AB. Magnetization-to-singlet-to-magnetization conversion has been performed using the SLIC and APSOC techniques, providing a degree of conversion up to 17 and 24% of the initial magnetization, respectively. Our approach is useful for optimizing the performance of experiments with singlet LLSs; such LLSs can be exploited for preserving spin hyperpolarization, for probing slow molecular dynamics, slow chemical processes and also slow transport processes.