Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies

19F NMR in RNA structural biology: exploring structures, dynamics, and small molecule interactions

RNA molecules play essential roles in numerous biological pathways, making them attractive targets for drug discovery. Despite the challenges in developing small molecules targeting RNA, the success in developing compounds that modulate RNA function underscores its therapeutic potential. 19F NMR spectroscopy has emerged as a powerful tool in structural biology and drug discovery, particularly for studying macromolecular structures and ligand interactions. As RNA continues to gain prominence as a drug target, 19F NMR is expected to play a pivotal role in advancing RNA-focused drug discovery. This review describes the diverse applications of 19F NMR in RNA biology, including its use in characterizing RNA structures, probing molecular dynamics, identifying small-molecule binders, and investigating interaction mechanisms of small-molecule ligands. By providing detailed structural and ligand binding insights, 19F NMR will facilitate the discovery of RNA-targeting therapeutics and deepen our understanding of RNA modulatory mechanisms.

Synthesis and Characterization of Multilayer 3D Chiral Polymers with Enhanced Optical Properties

This study reports the synthesis of novel multilayer 3D chiral polymers using 2,2'-(2,7-Naphthalenediyl)bis[4,4,5,5-tetramethyl-1,3,2-dioxaborolane] and 1,8-dibronaphthalene along with its derivatives as key precursors. Comprehensive characterization was performed using nuclear magnetic resonance (NMR), gel permeation chromatography (GPC), photoluminescence, ultraviolet (UV) spectroscopy, scanning electron microscopy (SEM), polarimetry, dynamic light scattering (DLS), and thermogravimetric analysis (TGA). Notably, the polymers exhibited remarkable aggregation-induced emission (AIE) and aggregation-induced polarization (AIP) phenomena, revealing enhanced luminescence and optical activity in aggregated states. These findings underscore the potential of these chiral polymers for applications in optoelectronics and advanced sensing technologies, highlighting the intricate relationship between molecular structure and optical behavior.

Elucidating the solution structure of the monomolecular BCL2 RNA G-quadruplex: a new robust NMR assignment approach

5' untranslated regions (UTRs) of mRNA commonly feature G-quadruplexes (G4s), crucial for translational regulation and promising as drug targets to modulate gene expression. While NMR spectroscopy is well-suited for studying these motifs' structure and dynamics, their guanine-rich nature complicates resonance assignment due to high signal overlap. Exploiting the inherent rigidity of G4 cores, we developed a universally applicable assignment strategy for uniformly isotopically enriched G4 structures, relying solely on through-bond correlations to establish the G-tetrads. Applying this approach, we resolved the solution structures of two triple mutants of the RNA G4 in the 5' UTR of the human BCL2 proto-oncogene, one of the first natural monomolecular RNA G4 structures available to date. Comparative analysis with other RNA and DNA G4s reveals their notably compact and well-defined cores. Moreover, the sugar pucker geometries of the tetrad guanines are far less stringent than previously assumed, adeptly accommodating specific structural features. This contrasts with the canonical base pairing in RNA and DNA, in which the sugar pucker dictates the type of the double-helical structure. The strategy presented provides a direct path to uncovering G4 structural intricacies, advancing our grasp of their biological roles, and paving the way for RNA-targeted therapeutics.

Gram-scale enzymatic synthesis of 2'-deoxyribonucleoside analogues using nucleoside transglycosylase-2

Nucleosides are pervasive building blocks that are found throughout nature and used extensively in medicinal chemistry and biotechnology. However, the preparation of base-modified analogues using conventional synthetic methodology poses challenges in scale-up and purification. In this work, an integrated approach involving structural analysis, screening and reaction optimization, is established to prepare 2'-deoxyribonucleoside analogues catalysed by the type II nucleoside 2'-deoxyribosyltransferase from Lactobacillus leichmannii (LlNDT-2). Structural analysis in combination with substrate profiling, identified the constraints on pyrimidine and purine acceptor bases by LlNDT2. A solvent screen identifies pure water as a suitable solvent for the preparation of high value purine and pyrimidine 2'-deoxyribonucleoside analogues on a gram scale under optimized reaction conditions. This approach provides the basis to establish a convergent, step-efficient chemoenzymatic platform for the preparation of high value 2'-deoxyribonucleosides.

Extending the toolbox for RNA biology with SegModTeX: a polymerase-driven method for site-specific and segmental labeling of RNA

RNA performs a wide range of functions regulated by its structure, dynamics, and often post-transcriptional modifications. While NMR is the leading method for understanding RNA structure and dynamics, it is currently limited by the inability to reduce spectral crowding by efficient segmental labeling. Furthermore, because of the challenging nature of RNA chemistry, the tools being developed to introduce site-specific modifications are increasingly complex and laborious. Here we use a previously designed Tgo DNA polymerase mutant to present SegModTeX - a versatile, one-pot, copy-and-paste approach to address these challenges. By precise, stepwise construction of a diverse set of RNA molecules, we demonstrate the technique to be superior to RNA polymerase driven and ligation methods owing to its substantially high yield, fidelity, and selectivity. We also show the technique to be useful for incorporating some fluorescent- and a wide range of other probes, which significantly extends the toolbox of RNA biology in general.

RNA structure determination: From 2D to 3D

RNA molecules serve a wide range of functions that are closely linked to their structures. The basic structural units of RNA consist of single- and double-stranded regions. In order to carry out advanced functions such as catalysis and ligand binding, certain types of RNAs can adopt higher-order structures. The analysis of RNA structures has progressed alongside advancements in structural biology techniques, but it comes with its own set of challenges and corresponding solutions. In this review, we will discuss recent advances in RNA structure analysis techniques, including structural probing methods, X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy, and small-angle X-ray scattering. Often, a combination of multiple techniques is employed for the integrated analysis of RNA structures. We also survey important RNA structures that have been recently determined using various techniques.

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.

Syntheses of Specifically 15 N‐Labeled Adenosine and Guanosine

This article describes the specific incorporation of ¹⁵ N into the N7 and amino positions of adenosine (Basic Protocol 1), and conversion of the adenosine to guanosine labeled at the N1, N7, and amino positions (Basic Protocol 2). Two variations of the procedures are also presented that include either ¹² C or ¹³ C at the C8 position of adenosine, and ¹³ C at either the C8 or C2 position of guanosine. These ¹³ C tags permit the incorporation of two ¹⁵ N-labeled nucleosides into an RNA strand while ensuring that their nuclear magnetic resonance (NMR) signals can be distinguished from each other by the presence or absence of C-N coupling. While the major application of these specifically ¹⁵ N-labeled nucleosides is NMR, the additional mass makes them useful in mass spectrometry (MS) as well. The procedures can also be adapted to synthesize the labeled deoxynucleosides. The Support Protocol describes the synthesis of 7-methylguanosine. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Syntheses of [7,NH₂ -¹⁵ N₂ ]- and [8-¹³ C-7,NH₂ -¹⁵ N₂ ]adenosine Support Protocol: Synthesis of 7-methylguanosine Basic Protocol 2: Synthesis of [2-¹³ C-1,7,NH₂ -¹⁵ N₃ ]- and [8-¹³ C-1,7,NH₂ -¹⁵ N₃ ]guanosine.

Mapping endocrine networks by stable isotope tracing

Hormones regulate metabolic homeostasis through interlinked dynamic networks of proteins and small molecular weight metabolites, and state-of-the-art chemical technologies have been developed to decipher these complex pathways. Stable-isotope tracers have largely replaced radiotracers to measure flux in humans, building on advances in nuclear magnetic resonance spectroscopy and mass spectrometry. These technologies are now being applied to localise molecules within tissues. Radiotracers are still highly valuable both preclinically and in 3D imaging by positron emission tomography. The coming of age of vibrational spectroscopy in conjunction with stable-isotope tracing offers detailed cellular insights to map complex biological processes. Together with computational modelling, these approaches are poised to coalesce into multi-modal platforms to provide hitherto inaccessible dynamic and spatial insights into endocrine signalling.

Enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR

Solution NMR spectroscopy is a well-established tool with unique advantages for structural studies of RNA molecules. However, for large RNA sequences, the NMR resonances often overlap severely. A reliable way to perform resonance assignment and allow further analysis despite spectral crowding is the use of site-specific isotope labeling in sample preparation. While solid-phase oligonucleotide synthesis has several advantages, RNA length and availability of isotope-labeled building blocks are persistent issues. Purely enzymatic methods represent an alternative and have been presented in the literature. In this study, we report on a method in which we exploit the preference of T7 RNA polymerase for nucleotide monophosphates over triphosphates for the 5’ position, which allows 5’-labeling of RNA. Successive ligation to an unlabeled RNA strand generates a site-specifically labeled RNA. We show the successful production of such an RNA sample for NMR studies, report on experimental details and expected yields, and present the surprising finding of a previously hidden set of peaks which reveals conformational exchange in the RNA structure. This study highlights the feasibility of site-specific isotope-labeling of RNA with enzymatic methods.

Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs

RNA is central to the proper function of cellular processes important for life on earth and implicated in various medical dysfunctions. Yet, RNA structural biology lags significantly behind that of proteins, limiting mechanistic understanding of RNA chemical biology. Fortunately, solution NMR spectroscopy can probe the structural dynamics of RNA in solution at atomic resolution, opening the door to their functional understanding. However, NMR analysis of RNA, with only four unique ribonucleotide building blocks, suffers from spectral crowding and broad linewidths, especially as RNAs grow in size. One effective strategy to overcome these challenges is to introduce NMR-active stable isotopes into RNA. However, traditional uniform labeling methods introduce scalar and dipolar couplings that complicate the implementation and analysis of NMR measurements. This challenge can be circumvented with selective isotope labeling. In this review, we outline the development of labeling technologies and their application to study biologically relevant RNAs and their complexes ranging in size from 5 to 300 kDa by NMR spectroscopy.