The influence of sample mass (scaling effect) on the synthesis and structure of non-graphitizing carbon (biochar) during the analytical pyrolysis of biomass.

The porous non-graphitizing carbon (NGC) known as biochar is derived from the pyrolytic conversion of organic precursors and is widely investigated due to its multifunctional applications. At present, biochar is predominantly synthesized in custom lab-scale reactors (LSRs) to determine the properties of carbon, while a thermogravimetric reactor (TG) is utilized for pyrolysis characterization. This results in inconsistencies in the correlation between the structure of biochar carbon and the pyrolysis process. If a TG reactor can also be used as an LSR for biochar synthesis, then the process characteristics and the properties of the synthesized NGC can be simultaneously investigated. It also eliminates the need for expensive LSRs in the laboratory, improves the reproducibility, and correlatability of pyrolysis characteristics with the properties of the resulting biochar carbon. Furthermore, despite numerous TG studies on the kinetics and characterization of biomass pyrolysis, none have questioned how the properties of biochar carbon vary due to the influence of the starting sample mass (scaling) in the reactor. Herein, with a lignin-rich model substrate (walnut shells), TG is utilized as an LSR, for the first time, to investigate the scaling effect starting from the pure kinetic regime (KR). The changes in the pyrolysis characteristics and the structural properties of the resultant NGC with scaling are concurrently traced and comprehensively studied. It is conclusively proven that scaling influences the pyrolysis process and the NGC structure. There is a gradual shift in pyrolysis characteristics and NGC properties from the KR until an inflection mass of ∼200 mg is reached. After this, the carbon properties (aryl-C%, pore characteristics, defects in nanostructure, and biochar yield) are similar. At small scales (≲100 mg), and especially near the KR (≤10 mg) carbonization is higher despite the reduced char formation reaction. The pyrolysis is more endothermic near KR with increased emissions of CO2 and H2O. For a lignin-rich precursor, at masses above inflection point, TG can be employed for concurrent pyrolysis characterization and biochar synthesis for application-specific NGC investigations.

Specific Signal Enhancement on an RNA-Protein Interface by Dynamic Nuclear Polarization.

Invited for the cover of this issue are the groups of Alexander Marchanka at the Leibniz University of Hannover and Björn Corzilius at the University of Rostock. The image depicts the local generation of nuclear spin hyperpolarization, which selectively "illuminates" the interaction surface of a ribonuclear protein complex for solid-state NMR spectroscopy. Read the full text of the article at 10.1002/chem.202203443.

Specific Signal Enhancement on an RNA-Protein Interface by Dynamic Nuclear Polarization.

Sensitivity and specificity are both crucial for the efficient solid-state NMR structure determination of large biomolecules. We present an approach that features both advantages by site-specific enhancement of NMR spectroscopic signals from the protein-RNA binding site within a ribonucleoprotein (RNP) by dynamic nuclear polarization (DNP). This approach uses modern biochemical techniques for sparse isotope labeling and exploits the molecular dynamics of 13 C-labeled methyl groups exclusively present in the protein. These dynamics drive heteronuclear cross relaxation and thus allow specific hyperpolarization transfer across the biomolecular complex's interface. For the example of the L7Ae protein in complex with a 26mer guide RNA minimal construct from the box C/D complex in archaea, we demonstrate that a single methyl-nucleotide contact is responsible for most of the polarization transfer to the RNA, and that this specific transfer can be used to boost both NMR spectral sensitivity and specificity by DNP.

Nucleic acid-protein interfaces studied by MAS solid-state NMR spectroscopy.

Solid-state NMR (ssNMR) has become a well-established technique to study large and insoluble protein assemblies. However, its application to nucleic acid-protein complexes has remained scarce, mainly due to the challenges presented by overlapping nucleic acid signals. In the past decade, several efforts have led to the first structure determination of an RNA molecule by ssNMR. With the establishment of these tools, it has become possible to address the problem of structure determination of nucleic acid-protein complexes by ssNMR. Here we review first and more recent ssNMR methodologies that study nucleic acid-protein interfaces by means of chemical shift and peak intensity perturbations, direct distance measurements and paramagnetic effects. At the end, we review the first structure of an RNA-protein complex that has been determined from ssNMR-derived intermolecular restraints.

Strategies for RNA Resonance Assignment by 13C/15N- and 1H-Detected Solid-State NMR Spectroscopy.

Magic angle spinning (MAS) solid-state NMR (ssNMR) is an established tool that can be applied to non-soluble or non-crystalline biomolecules of any size or complexity. The ssNMR method advances rapidly due to technical improvements and the development of advanced isotope labeling schemes. While ssNMR has shown significant progress in structural studies of proteins, the number of RNA studies remains limited due to ssNMR methodology that is still underdeveloped. Resonance assignment is the most critical and limiting step in the structure determination protocol that defines the feasibility of NMR studies. In this review, we summarize the recent progress in RNA resonance assignment methods and approaches for secondary structure determination by ssNMR. We critically discuss advantages and limitations of conventional 13C- and 15N-detected experiments and novel 1H-detected methods, identify optimal regimes for RNA studies by ssNMR, and provide our view on future ssNMR studies of RNA in large RNP complexes.

Identification of RNA Base Pairs and Complete Assignment of Nucleobase Resonances by Proton-Detected Solid-State NMR Spectroscopy at 100†kHz MAS.

Knowledge of RNA structure, either in isolation or in complex, is fundamental to understand the mechanism of cellular processes. Solid-state NMR (ssNMR) is applicable to high molecular-weight complexes and does not require crystallization; thus, it is well-suited to study RNA as part of large multicomponent assemblies. Recently, we solved the first structures of both RNA and an RNA-protein complex by ssNMR using conventional 13 C- and 15 N-detection. This approach is limited by the severe overlap of the RNA peaks together with the low sensitivity of multidimensional experiments. Here, we overcome the limitations in sensitivity and resolution by using 1 H-detection at fast MAS rates. We develop experiments that allow the identification of complete nucleobase spin-systems together with their site-specific base pair pattern using sub-milligram quantities of one uniformly labelled RNA sample. These experiments provide rapid access to RNA secondary structure by ssNMR in protein-RNA complexes of any size.

Solid-state NMR spectroscopy for characterization of RNA and RNP complexes.

Ribonucleic acids are driving a multitude of biological processes where they act alone or in complex with proteins (ribonucleoproteins, RNP). To understand these processes both structural and mechanistic information about RNA is necessary. Due to their conformational plasticity RNA pose a challenge for mainstream structural biology methods. Solid-state NMR (ssNMR) spectroscopy is an emerging technique that can be applied to biomolecular complexes of any size in close-to-native conditions. This review outlines recent methodological developments in ssNMR for structural characterization of RNA and protein-RNA complexes and provides relevant examples.

Structure of a Protein-RNA Complex by Solid-State NMR Spectroscopy.

Solid-state NMR (ssNMR) is applicable to high molecular-weight (MW) protein assemblies in a non-amorphous precipitate. The technique yields atomic resolution structural information on both soluble and insoluble particles without limitations of MW or requirement of crystals. Herein, we propose and demonstrate an approach that yields the structure of protein-RNA complexes (RNP) solely from ssNMR data. Instead of using low-sensitivity magnetization transfer steps between heteronuclei of the protein and the RNA, we measure paramagnetic relaxation enhancement effects elicited on the RNA by a paramagnetic tag coupled to the protein. We demonstrate that this data, together with chemical-shift-perturbation data, yields an accurate structure of an RNP complex, starting from the bound structures of its components. The possibility of characterizing protein-RNA interactions by ssNMR may enable applications to large RNP complexes, whose structures are not accessible by other methods.

Solid-State NMR Spectroscopy of RNA.

RNA structure is essential to understand RNA function and regulation in cellular processes. RNA acts either in isolation or as part of a complex with proteins. Both isolated and protein-complexed RNA represent a challenge for structural biology, due to the complexity of its conformational space and intrinsic dynamics. NMR, with its capability to cope with dynamic structures, is the optimal technique to study RNA conformation, ideally in solution. However, RNA-protein complexes are often very large, which limits the application of solution-state NMR. In this chapter we describe the methodology that we developed to determine the structure of RNA by solid-state NMR. Solid-state NMR is not limited by large molecular weights and can be optimally applied to study both the RNA and the protein components of large RNA-protein complexes. We review the methods for resonance assignments, collection of RNA-specific distance restraints, as well as detection of protein-RNA interfaces.

Rapid access to RNA resonances by proton-detected solid-state NMR at >100 kHz MAS.

Fast (>100 kHz) magic angle spinning solid-state NMR allows combining high-sensitive proton detection with the absence of an intrinsic molecular weight limit. Using this technique we observe for the first time narrow 1H RNA resonances and assign nucleotide spin systems with only 200 µg of uniformly 13C,15N-labelled RNA.

Isotope labeling for studying RNA by solid-state NMR spectroscopy.

Nucleic acids play key roles in most biological processes, either in isolation or in complex with proteins. Often they are difficult targets for structural studies, due to their dynamic behavior and high molecular weight. Solid-state nuclear magnetic resonance spectroscopy (ssNMR) provides a unique opportunity to study large biomolecules in a non-crystalline state at atomic resolution. Application of ssNMR to RNA, however, is still at an early stage of development and presents considerable challenges due to broad resonances and poor dispersion. Isotope labeling, either as nucleotide-specific, atom-specific or segmental labeling, can resolve resonance overlaps and reduce the line width, thus allowing ssNMR studies of RNA domains as part of large biomolecules or complexes. In this review we discuss the methods for RNA production and purification as well as numerous approaches for isotope labeling of RNA. Furthermore, we give a few examples that emphasize the instrumental role of isotope labeling and ssNMR for studying RNA as part of large ribonucleoprotein complexes.

RNA structure determination by solid-state NMR spectroscopy.

Knowledge of the RNA three-dimensional structure, either in isolation or as part of RNP complexes, is fundamental to understand the mechanism of numerous cellular processes. Because of its flexibility, RNA represents a challenge for crystallization, while the large size of cellular complexes brings solution-state NMR to its limits. Here, we demonstrate an alternative approach on the basis of solid-state NMR spectroscopy. We develop a suite of experiments and RNA labeling schemes and demonstrate for the first time that ssNMR can yield a RNA structure at high-resolution. This methodology allows structural analysis of segmentally labelled RNA stretches in high-molecular weight cellular machines­independent of their ability to crystallize­and opens the way to mechanistic studies of currently difficult-to-access RNA-protein assemblies.

A suite of solid-state NMR experiments for RNA intranucleotide resonance assignment in a 21 kDa protein-RNA complex.

Intranucleotide resonance of the 26mer box C/D RNA in complex with the L7Ae protein were assigned by solid-state NMR (ssNMR; see picture) spectroscopy. This investigation opens the way for studying RNA in large protein-RNA complexes by ssNMR spectroscopy.