A 300-fold enhancement of imino nucleic acid resonances by hyperpolarized water provides a new window for probing RNA refolding by 1D and 2D NMR

Hyperpolarized nuclear Overhauser enhancement of alanine methyl groups by doubly relayed proton exchange

Hyperpolarized water in dissolution dynamic nuclear polarization (dDNP) experiments has emerged as a promising method for enhancing nuclear magnetic resonance (NMR) signals, particularly in studies of proteins and peptides. Herein, we focus on the application of "proton exchange-doubly relayed" nuclear Overhauser effects (NOE) from hyperpolarized water to achieve positive signal enhancement of methyl groups in the side chain of an alanine-glycine peptide. In particular, we show a cascade hyperpolarization transfer. Initial proton exchange between solvent and amide introduces hyperpolarization into the peptide. Subsequently, intermolecular NOE relays the hyperpolarization first to Ala-Hα and then in a second step to the Ala-CH3 moiety. Both NOEs have negative signs. Hence, the twice-relayed NOE pathway leads to a positive signal enhancement of the methyl group with respect to the thermal equilibrium magnetization. This effect might indicate a way towards hyperpolarized water-based signal enhancement for methyl groups, which are often used for NMR studies of large proteins in solution.

NMR of RNA - Structure and interactions

RNA was shown to have a more substantial role in the regulation of diverse cellular processes than anticipated until recently. Answers to questions what is the structure of specific RNAs, how structure changes to accommodate different functional roles, and how RNA senses other biomolecules and changes its fold upon interaction create a complete representation of RNA involved in cellular processes. Nuclear magnetic resonance (NMR) spectroscopy encompasses a collection of methods and approaches that offer insight into several structural aspects of RNAs. We review the most recent advances in the field of viral, long non-coding, regulatory, and four-stranded RNAs, with an emphasis on the detection of dynamic sub-states and in view of chemical modifications that expand RNA's function.

Missing Pieces in Structure Puzzles: How Hyperpolarized NMR Spectroscopy Can Complement Structural Biology and Biochemistry

Structure determination lies at the heart of many biochemical research programs. However, the "giants": X-ray diffraction, electron microscopy, molecular dynamics simulations, and nuclear magnetic resonance, among others, leave quite a few dark spots on the structural pictures drawn of proteins, nucleic acids, membranes, and other biomacromolecules. For example, structural models under physiological conditions or of short-lived intermediates often remain out of reach of the established experimental methods. This account frames the possibility of including hyperpolarized, that is, dramatically signal-enhanced NMR in existing workflows to fill these spots with detailed depictions. We highlight how integrating methods based on dissolution dynamic nuclear polarization can provide valuable complementary information about formerly inaccessible conformational spaces for many systems. A particular focus will be on hyperpolarized buffers to facilitate the NMR structure determination of challenging systems.

Discovery of RNA-targeted small molecules through the merging of experimental and computational technologies

INTRODUCTION

The field of RNA-targeted small molecules is rapidly evolving, owing to the advances in experimental and computational technologies. With the identification of several bioactive small molecules that target RNA, including the FDA-approved risdiplam, the biopharmaceutical industry is gaining confidence in the field. This review, based on the literature obtained from PubMed, aims to disseminate information about the various technologies developed for targeting RNA with small molecules and propose areas for improvement to develop drugs more efficiently, particularly those linked to diseases with unmet medical needs.

AREAS COVERED

The technologies for the identification of RNA targets, screening of chemical libraries against RNA, assessing the bioactivity and target engagement of the hit compounds, structure determination, and hit-to-lead optimization are reviewed. Along with the description of the technologies, their strengths, limitations, and examples of how they can impact drug discovery are provided.

EXPERT OPINION

Many existing technologies employed for protein targets have been repurposed for use in the discovery of RNA-targeted small molecules. In addition, technologies tailored for RNA targets have been developed. Nevertheless, more improvements are necessary, such as artificial intelligence to dissect important RNA structures and RNA-small-molecule interactions and more powerful chemical probing and structure prediction techniques.

Spin Hyperpolarization in Modern Magnetic Resonance

Magnetic resonance techniques are successfully utilized in a broad range of scientific disciplines and in various practical applications, with medical magnetic resonance imaging being the most widely known example. Currently, both fundamental and applied magnetic resonance are enjoying a major boost owing to the rapidly developing field of spin hyperpolarization. Hyperpolarization techniques are able to enhance signal intensities in magnetic resonance by several orders of magnitude, and thus to largely overcome its major disadvantage of relatively low sensitivity. This provides new impetus for existing applications of magnetic resonance and opens the gates to exciting new possibilities. In this review, we provide a unified picture of the many methods and techniques that fall under the umbrella term "hyperpolarization" but are currently seldom perceived as integral parts of the same field. Specifically, before delving into the individual techniques, we provide a detailed analysis of the underlying principles of spin hyperpolarization. We attempt to uncover and classify the origins of hyperpolarization, to establish its sources and the specific mechanisms that enable the flow of polarization from a source to the target spins. We then give a more detailed analysis of individual hyperpolarization techniques: the mechanisms by which they work, fundamental and technical requirements, characteristic applications, unresolved issues, and possible future directions. We are seeing a continuous growth of activity in the field of spin hyperpolarization, and we expect the field to flourish as new and improved hyperpolarization techniques are implemented. Some key areas for development are in prolonging polarization lifetimes, making hyperpolarization techniques more generally applicable to chemical/biological systems, reducing the technical and equipment requirements, and creating more efficient excitation and detection schemes. We hope this review will facilitate the sharing of knowledge between subfields within the broad topic of hyperpolarization, to help overcome existing challenges in magnetic resonance and enable novel applications.

Frémy’s Salt as a Low-Persistence Hyperpolarization Agent: Efficient Dynamic Nuclear Polarization Plus Rapid Radical Scavenging

Nuclear magnetic resonance (NMR) spectroscopy is a key technique for molecular structure determination in solution. However, due to its low sensitivity, many efforts have been made to improve signal strengths and reduce the required substrate amounts. In this regard, dissolution dynamic nuclear polarization (DDNP) is a versatile approach as signal enhancements of over 10 000-fold are achievable. Samples are signal-enhanced ex situ by transferring electronic polarization from radicals to nuclear spins before dissolving and shuttling the boosted sample to an NMR spectrometer for detection. However, the applicability of DDNP suffers from one major drawback, namely, paramagnetic relaxation enhancements (PREs) that critically reduce relaxation times due to the codissolved radicals. PREs are the primary source of polarization losses canceling the signal improvements obtained by DNP. We solve this problem by using potassium nitrosodisulfonate (Frémy’s salt) as polarization agent (PA), which provides high nuclear spin polarization and allows for rapid scavenging under mild reducing conditions. We demonstrate the potential of Frémy’s salt, (i) showing that both ¹H and ¹³C polarization of ∼30% can be achieved and (ii) describing a hybrid sample shuttling system (HySSS) that can be used with any DDNP/NMR combination to remove the PA before NMR detection. This gadget mixes the hyperpolarized solution with a radical scavenger and injects it into an NMR tube, providing, within a few seconds, quantitatively radical-free, highly polarized solutions. The cost efficiency and broad availability of Frémy’s salt might facilitate the use of DDNP in many fields of research.

Toward protein NMR at physiological concentrations by hyperpolarized water-Finding and mapping uncharted conformational spaces

Nuclear magnetic resonance (NMR) spectroscopy is a key method for determining the structural dynamics of proteins in their native solution state. However, the low sensitivity of NMR typically necessitates nonphysiologically high sample concentrations, which often limit the relevance of the recorded data. We show how to use hyperpolarized water by dissolution dynamic nuclear polarization (DDNP) to acquire protein spectra at concentrations of 1 μM within seconds and with a high signal-to-noise ratio. The importance of approaching physiological concentrations is demonstrated for the vital MYC-associated factor X, which we show to switch conformations when diluted. While in vitro conditions lead to a population of the well-documented dimer, concentrations lowered by more than two orders of magnitude entail dimer dissociation and formation of a globularly folded monomer. We identified this structure by integrating DDNP with computational techniques to overcome the often-encountered constraint of DDNP of limited structural information provided by the typically detected one-dimensional spectra.

Inversion of Hyperpolarized 13C NMR Signals through Cross-Correlated Cross-Relaxation in Dissolution DNP Experiments

Dissolution dynamic nuclear polarization (DDNP) is a versatile tool to boost signal amplitudes in solution-state nuclear magnetic resonance (NMR) spectroscopy. For DDNP, nuclei are spin-hyperpolarized "ex situ" in a dedicated DNP device and then transferred to an NMR spectrometer for detection. Dramatic signal enhancements can be achieved, enabling shorter acquisition times, real-time monitoring of fast reactions, and reduced sample concentrations. Here, we show how the sample transfer in DDNP experiments can affect NMR spectra through cross-correlated cross-relaxation (CCR), especially in the case of low-field passages. Such processes can selectively invert signals of ¹³C spins in proton-carrying moieties. For their investigations, we use schemes for simultaneous or "parallel" detection of hyperpolarized ¹H and ¹³C nuclei. We find that ¹H → ¹³C CCR can invert signals of ¹³C spins if the proton polarization is close to 100%. We deduce that low-field passage in a DDNP experiment, a common occurrence due to the introduction of so-called "ultra-shielded" magnets, accelerates these effects due to field-dependent paramagnetic relaxation enhancements that can influence CCR. The reported effects are demonstrated for various molecules, laboratory layouts, and DDNP systems. As coupled ¹³C-¹H spin systems are ubiquitous, we expect similar effects to be observed in various DDNP experiments. This might be exploited for selective spectroscopic labeling of hydrocarbons.

Interfacing Liquid State Hyperpolarization Methods with NMR Instrumentation

Advances in liquid state hyperpolarization methods have enabled new applications of high-resolution NMR spectroscopy. Utilizing strong signal enhancements from hyperpolarization allows performing NMR spectroscopy at low concentration, or with high time resolution. Making use of the high, but rapidly decaying hyperpolarization in the liquid state requires new techniques to interface hyperpolarization equipment with liquid state NMR spectrometers. This article highlights rapid injection, high resolution NMR spectroscopy with hyperpolarization produced by the techniques of dissolution dynamic nuclear polarization (D-DNP) and para-hydrogen induced polarization (PHIP). These are popular, albeit not the only methods to produce high polarization levels for liquid samples. Gas and liquid driven sample injection techniques are compatible with both of these hyperpolarization methods. The rapid sample injection techniques are combined with adapted NMR experiments working in a single, or small number of scans. They expand the application of liquid state hyperpolarization to spins with comparably short relaxation times, provide enhanced control over sample conditions, and allow for mixing experiments to study reactions in real time.

Hyperpolarized water as universal sensitivity booster in biomolecular NMR

NMR spectroscopy is the only method to access the structural dynamics of biomolecules at high (atomistic) resolution in their native solution state. However, this method's low sensitivity has two important consequences: (i) typically experiments have to be performed at high concentrations that increase sensitivity but are not physiological, and (ii) signals have to be accumulated over long periods, complicating the determination of interaction kinetics on the order of seconds and impeding studies of unstable systems. Both limitations are of equal, fundamental relevance: non-native conditions are of limited pharmacological relevance, and the function of proteins, enzymes and nucleic acids often relies on their interaction kinetics. To overcome these limitations, we have developed applications that involve 'hyperpolarized water' to boost signal intensities in NMR of proteins and nucleic acids. The technique includes four stages: (i) preparation of the biomolecule in partially deuterated buffers, (ii) preparation of 'hyperpolarized' water featuring enhanced ¹H NMR signals via cryogenic dynamic nuclear polarization, (iii) sudden melting of the cryogenic pellet and dissolution of the protein or nucleic acid in the hyperpolarized water (enabling spontaneous exchanges of protons between water and target) and (iv) recording signal-amplified NMR spectra targeting either labile ¹H or neighboring ¹⁵N/¹³C nuclei in the biomolecule. Water in the ensuing experiments is used as a universal 'hyperpolarization' agent, rendering the approach versatile and applicable to any biomolecule possessing labile hydrogens. Thus, questions can be addressed, ranging from protein and RNA folding problems to resolving structure-function relationships of intrinsically disordered proteins to investigating membrane interactions.

Frozen water NMR lineshape analysis enables absolute polarization quantification

Typical magnetic resonance experiments are routinely limited by weak signal responses. In some cases, the low intrinsic sensitivity can be alleviated by the implementation of hyperpolarization technologies. Dissolution-dynamic nuclear polarization offers a means of hyperpolarizing small molecules. Hyperpolarized water is employed in several dynamic nuclear polarization studies, and hence accurate and rapid quantification of the ¹H polarization level is of utmost importance. The solid-state nuclear magnetic resonance spectrum of water acquired under dissolution-dynamic nuclear polarization conditions has revealed lineshapes which become asymmetric at high levels of ¹H polarization, which is an interesting fundamental problem in itself, but also complicates data interpretation and can prevent correct estimations of polarization levels achieved. In previous studies, attempts to simulate the ¹H spectral lineshape of water as a function of the ¹H polarization led to significant disagreement with the experimental results. Here we propose and demonstrate that such simulations, and therefore polarization quantification, can be implemented accurately, in particular by taking into account the detector dead time during ¹H signal acquisition that can lead to severe spectral distortions. Based on these findings, we employed an echo-based radiofrequency pulse sequence to achieve distortion-free ¹H spectra of hyperpolarized water, and adequate simulations of these echo-based spectra were implemented to extract the absolute ¹H polarization level from the hyperpolarized water signal only, thus alleviating the need for lengthy and insensitive measurements of thermal equilibrium signals.

Room-temperature dynamic nuclear polarization enhanced NMR spectroscopy of small biological molecules in water

Nuclear magnetic resonance (NMR) spectroscopy is a powerful and popular technique for probing the molecular structures, dynamics and chemical properties. However the conventional NMR spectroscopy is bottlenecked by its low sensitivity. Dynamic nuclear polarization (DNP) boosts NMR sensitivity by orders of magnitude and resolves this limitation. In liquid-state this revolutionizing technique has been restricted to a few specific non-biological model molecules in organic solvents. Here we show that the carbon polarization in small biological molecules, including carbohydrates and amino acids, can be enhanced sizably by in situ Overhauser DNP (ODNP) in water at room temperature and at high magnetic field. An observed connection between ODNP 13C enhancement factor and paramagnetic 13C NMR shift has led to the exploration of biologically relevant heterocyclic compound indole. The QM/MM MD simulation underscores the dynamics of intermolecular hydrogen bonds as the driving force for the scalar ODNP in a long-living radical-substrate complex. Our work reconciles results obtained by DNP spectroscopy, paramagnetic NMR and computational chemistry and provides new mechanistic insights into the high-field scalar ODNP.

A cryogen-free, semi-automated apparatus for bullet-dynamic nuclear polarization with improved resolution

In dissolution-dynamic nuclear polarization, a hyperpolarized solid is dissolved with a jet of hot solvent. The solution is then transferred to a secondary magnet, where spectra can be recorded with improved sensitivity. In bullet-dynamic nuclear polarization this order is reversed. Pressurized gas is used to rapidly transfer the hyperpolarized solid to the secondary magnet, and the hyperpolarized solid is dissolved only upon arrival. A potential advantage of this approach is that it may avoid excessive dilution and the associated signal loss, in particular for small sample quantities. Previously, we have shown that liquid-state NMR spectra with polarization levels of up to 30 % may be recorded within less than 1 s after the departure of the hyperpolarized solid from the polarizing magnet. The resolution of the recorded spectra however was limited. The system consumed significant amounts of liquid helium, and substantial manual work was required in between experiments to prepare for the next shot. Here, we present a new bullet-DNP (dynamic nuclear polarization) system that addresses these limitations.

Parahydrogen-Induced Polarization of Amino Acids

Nuclear magnetic resonance (NMR) has become a universal method for biochemical and biomedical studies, including metabolomics, proteomics, and magnetic resonance imaging (MRI). By increasing the signal of selected molecules, the hyperpolarization of nuclear spin has expanded the reach of NMR and MRI even further (e.g. hyperpolarized solid-state NMR and metabolic imaging in vivo). Parahydrogen (pH2 ) offers a fast and cost-efficient way to achieve hyperpolarization, and the last decade has seen extensive advances, including the synthesis of new tracers, catalysts, and transfer methods. The portfolio of hyperpolarized molecules now includes amino acids, which are of great interest for many applications. Here, we provide an overview of the current literature and developments in the hyperpolarization of amino acids and peptides.

Residue-resolved monitoring of protein hyperpolarization at sub-second time resolution

Signal-enhancement techniques for NMR spectroscopy are important to amplify the weak resonances provided by nuclear spins. Recently, 'hyperpolarization' techniques have been intensively investigated. These provide nuclear spin states far from equilibrium yielding strong signal boosts up to four orders of magnitude. Here we propose a method for real-time NMR of 'hyperpolarized' proteins at residue resolution. The approach is based on dissolution dynamic nuclear polarization (d-DNP), which enables the use of hyperpolarized buffers that selectively boost NMR signals of solvent-exposed protein residues. The resulting spectral sparseness and signal enhancements enable recording of residue-resolved spectra at a 2 Hz sampling rate. Thus, we monitor the hyperpolarization level of different protein residues simultaneously under near-physiological conditions. We aim to address two points: 1) NMR experiments are often performed under conditions that increase sensitivity but are physiologically irrelevant; 2) long signal accumulation impedes fast real-time monitoring. Both limitations are of fundamental relevance to ascertain pharmacological relevance and study protein kinetics.

Characterization of protein-ligand interactions by SABRE

Nuclear spin hyperpolarization through signal amplification by reversible exchange (SABRE), the non-hydrogenative version of para-hydrogen induced polarization, is demonstrated to enhance sensitivity for the detection of biomacromolecular interactions. A target ligand for the enzyme trypsin includes the binding motif for the protein, and at a distant location a heterocyclic nitrogen atom for interacting with a SABRE polarization transfer catalyst. This molecule, 4-amidinopyridine, is hyperpolarized with 50% para-hydrogen to yield enhancement values ranging from −87 and −34 in the ortho and meta positions of the heterocyclic nitrogen, to −230 and −110, for different solution conditions. Ligand binding is identified by flow-NMR, in a two-step process that separately optimizes the polarization transfer in methanol while detecting the interaction in a predominantly aqueous medium. A single scan Carr–Purcell–Meiboom–Gill (CPMG) experiment identifies binding by the change in R₂ relaxation rate. The SABRE hyperpolarization technique provides a cost effective means to enhance NMR of biological systems, for the identification of protein–ligand interactions and other applications.

Protein–ligand binding interactions are characterized by the para-H₂ based hyperpolarization technique SABRE and flow-NMR. Binding to the protein is identified by R₂ change of a ligand first interacting with the Ir polarization transfer catalyst.

Spontaneous Enhancement of Magnetic Resonance Signals Using a RASER

Nuclear magnetic resonance is usually drastically limited by its intrinsically low sensitivity: Only a few spins contribute to the overall signal. To overcome this limitation, hyperpolarization methods were developed that increase signals several times beyond the normal/thermally polarized signals. The ideal case would be a universal approach that can signal enhance the complete sample of interest in solution to increase detection sensitivity. Here, we introduce a combination of para-hydrogen enhanced magnetic resonance with the phenomenon of the RASER: Large signals of para-hydrogen enhanced molecules interact with the magnetic resonance coil in a way that the signal is spontaneously converted into an in-phase signal. These molecules directly interact with other compounds via dipolar couplings and enhance their signal. We demonstrate that this is not only possible for solvent molecules but also for an amino acid.

Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics

The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.

Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids

Nucleic acids do not fold into a single conformation, and dynamic ensembles are needed to describe their propensities to cycle between different conformations when performing cellular functions. We review recent advances in solution-state nuclear magnetic resonance (NMR) methods and their integration with computational techniques that are improving the ability to probe the dynamic ensembles of DNA and RNA. These include computational approaches for predicting chemical shifts from structure and generating conformational libraries from sequence, measurements of exact nuclear Overhauser effects, development of new probes to study chemical exchange using relaxation dispersion, faster and more sensitive real-time NMR techniques, and new NMR approaches to tackle large nucleic acid assemblies. We discuss how these advances are leading to new mechanistic insights into gene expression and regulation.

NMR spectroscopy captures the essential role of dynamics in regulating biomolecular function

Biomolecules are in constant motion. To understand how they function, and why malfunctions can cause disease, it is necessary to describe their three-dimensional structures in terms of dynamic conformational ensembles. Here, we demonstrate how nuclear magnetic resonance (NMR) spectroscopy provides an essential, dynamic view of structural biology that captures biomolecular motions at atomic resolution. We focus on examples that emphasize the diversity of biomolecules and biochemical applications that are amenable to NMR, such as elucidating functional dynamics in large molecular machines, characterizing transient conformations implicated in the onset of disease, and obtaining atomic-level descriptions of intrinsically disordered regions that make weak interactions involved in liquid-liquid phase separation. Finally, we discuss the pivotal role that NMR has played in driving forward our understanding of the biomolecular dynamics-function paradigm.

Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy

The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5' end, the ribosomal frameshift segment and the 3'-untranslated region (3'-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.

Hyperpolarized water through dissolution dynamic nuclear polarization with UV-generated radicals

In recent years, hyperpolarization of water protons via dissolution Dynamic Nuclear Polarization (dDNP) has attracted increasing interest in the magnetic resonance community. Hyperpolarized water may provide an alternative to Gd-based contrast agents for angiographic and perfusion Magnetic Resonance Imaging (MRI) examinations, and it may report on chemical and biochemical reactions and proton exchange while perfoming Nuclear Magnetic Resonance (NMR) investigations. However, hyperpolarizing water protons is challenging. The main reason is the presence of radicals, required to create the hyperpolarized nuclear spin state. Indeed, the radicals will also be the main source of relaxation during the dissolution and transfer to the NMR or MRI system. In this work, we report water magnetizations otherwise requiring a field of 10,000 T at room temperature on a sample of pure water, by employing dDNP via UV-generated, labile radicals. We demonstrate the potential of our methodology by acquiring a ¹⁵N spectrum from natural abundance urea with a single scan, after spontaneous magnetization transfer from water protons to nitrogen nuclei.