Self‐Assembly of DNA and RNA Building Blocks Explored by Nitrogen‐14 NMR Crystallography: Structure and Dynamics

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.

Combining heteronuclear correlation NMR with spin-diffusion to detect relayed Cl-H-H and N-H-H proximities in molecular solids

Analysis of short-to-intermediate range intermolecular interactions offers a great way of characterizing the solid-state organization of small molecules and materials. This can be achieved by two-dimensional (2D) homo- and heteronuclear correlation NMR spectroscopy, for example, by carrying out experiments at high magnetic fields in conjunction with fast magic-angle spinning (MAS) techniques. But, detecting 2D peaks for heteronuclear dipolar coupled spin pairs separated by greater than 3 Å is not always straightforward, particularly when low-gamma quadrupolar nuclei are involved. Here, we present a 2D correlation NMR experiment that combines the advantages of heteronuclear-multiple quantum coherence (HMQC) and proton-based spin-diffusion (SD) pulse sequences using radio-frequency-driven-recouping (RFDR) to probe inter and intramolecular ¹H-X (X = ¹⁴N, ³⁵Cl) interactions. This experiment can be used to acquire 2D ¹H{X}-HMQC filtered ¹H-¹H correlation as well as 2D ¹H-X HMQC spectra. Powder forms of dopamine·HCl and l-histidine·HCl·H₂O are characterized at high fields (21.1 T and 18.8 T) with fast MAS (60 kHz) using the 2D HMQC-SD-RFDR approach. Solid-state NMR results are complemented with NMR crystallography analyses using the gauge-including projector augmented wave (GIPAW) approach. For histidine·HCl·H₂O, 2D peaks associated with ¹⁴N-¹H-¹H and ³⁵Cl-¹H-¹H distances of up to 4.4 and 3.9 Å have been detected. This is further corroborated by the observation of 2D peaks corresponding to ¹⁴N-¹H-¹H and ³⁵Cl-¹H-¹H distances of up to 4.2 and 3.7 Å in dopamine·HCl, indicating the suitability of the HMQC-SD-RFDR experiments for detecting medium-range proximities in molecular solids.

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.

Enzymatic construction of metal-mediated nucleic acid base pairs

Artificial metal base pairs have become increasingly important in nucleic acids chemistry due to their high thermal stability, water solubility, orthogonality to natural base pairs, and low cost of production. These interesting properties combined with ease of chemical and enzymatic synthesis have prompted their use in several practical applications, including the construction of nanomolecular devices, ions sensors, and metal nanowires. Chemical synthesis of metal base pairs is highly efficient and enables the rapid screening of novel metal base pair candidates. However, chemical synthesis is limited to rather short oligonucleotides and requires rather important synthetic efforts. Herein, we discuss recent progress made for the enzymatic construction of metal base pairs that can alleviate some of these limitations. First, we highlight the possibility of generating metal base pairs using canonical nucleotides and then describe how modified nucleotides can be used in this context. We also provide a description of the main analytical techniques used for the analysis of the nature and the formation of metal base pairs together with relevant examples of their applications.

Natural abundance oxygen-17 solid-state NMR of metal organic frameworks enhanced by dynamic nuclear polarization

The 17O resonances of zirconium-oxo clusters that can be found in porous Zr carboxylate metal-organic frameworks (MOFs) have been investigated by magic-angle spinning (MAS) NMR spectroscopy enhanced by dynamic nuclear polarization (DNP). High-resolution 17O spectra at 0.037% natural abundance could be obtained in 48 hours, thanks to DNP enhancement of the 1H polarization by factors ε(1H) = Swith/Swithout = 28, followed by 1H → 17O cross-polarization, allowing a saving in experimental time by a factor of ca. 800. The distinct 17O sites from the oxo-clusters can be resolved at 18.8 T. Their assignment is supported by density functional theory (DFT) calculations of chemical shifts and quadrupolar parameters. Protonation of 17O sites seems to be leading to large characteristic shifts. Hence, natural abundance 17O NMR spectra of diamagnetic MOFs can thus be used to probe and characterize the local environment of different 17O sites on an atomic scale.

Effective Hamiltonian and 1H-14N cross polarization/double cross polarization at fast MAS

In this work we investigate in detail the underlying spin-dynamics associated with ¹H-¹⁴N double CP experiments under fast MAS, recently demonstrated by Carnevale et al. We employ matrix logarithm and Floquet theory to compute numerically the effective Hamiltonian associated to the time-dependent problem. Certain common features related to construction of effective Hamiltonians by both approaches are discussed. The main observations related to ¹H-¹⁴N CPMAS/double CP transfer are: (a) various spin terms of the effective Hamiltonian strongly depend on the crystallite orientation; (b) significant CP transfer occurs only when the magnitudes of the effective¹H and ¹⁴N RF strengths are comparable, and simultaneously all pure ¹⁴N terms in the effective Hamiltonian are small, except for the longitudinal and the RF terms; (c) the sign of ¹⁴N CPMAS signal follows the sign of ¹⁴N effective RF strength; (d) sign of the double CP signal is largely independent of crystallite orientation. We predict and verify matching conditions employing multiples of the spinning frequency or involving different ¹⁴N RF strengths. We provide an analytical proof for (d). The proof also provides an estimate for the ratio of ¹H-¹⁴N and ¹⁴N-¹H transfer amplitudes which is further substantiated through simulations. In addition, we find that double CP signals include contributions from several single-quantum coherences present after the first CP process. The uneven contribution from different coherences leads to a reversal of signal at very short contact times, a feature noted experimentally by Carnevale et al. The connection between CPMAS transfer and efficient spin-lock is discussed and illustrated. The factors affecting second-order quadrupolar lineshapes in double CP experiment are examined. With a linear ramp of ¹H RF amplitude we have observed that significant CP transfer occurs for more crystallite orientations resulting in improved sensitivity.