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

Pintér, György; Hohmann, Katharina F.; Grün, J. Tassilo; Wirmer‐Bartoschek, Julia; Glaubitz, Clemens; Fürtig, Boris; Schwalbe, Harald

doi:10.5194/mr-2-291-2021

Cited by 7 publications

(4 citation statements)

References 249 publications

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“…In Barraud et al (2019) , the authors describe the maturation of yeast tRNAPhe in cell culture extracts using labelled isotype in a continuous and time-resolved fashion. A general and extensive overview of real-time NMR spectroscopy methods, with an interesting focus on folding-inducing ligands, is reported in Pintér et al (2021) .…”

Section: Experimental Methods For the Study Of Rna Dynamics And Flexi...mentioning

confidence: 99%

An overview of structural approaches to study therapeutic RNAs

Mollica

Cupaioli²,

Rossetti³

et al. 2022

Front. Mol. Biosci.

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RNAs provide considerable opportunities as therapeutic agent to expand the plethora of classical therapeutic targets, from extracellular and surface proteins to intracellular nucleic acids and its regulators, in a wide range of diseases. RNA versatility can be exploited to recognize cell types, perform cell therapy, and develop new vaccine classes. Therapeutic RNAs (aptamers, antisense nucleotides, siRNA, miRNA, mRNA and CRISPR-Cas9) can modulate or induce protein expression, inhibit molecular interactions, achieve genome editing as well as exon-skipping. A common RNA thread, which makes it very promising for therapeutic applications, is its structure, flexibility, and binding specificity. Moreover, RNA displays peculiar structural plasticity compared to proteins as well as to DNA. Here we summarize the recent advances and applications of therapeutic RNAs, and the experimental and computational methods to analyze their structure, by biophysical techniques (liquid-state NMR, scattering, reactivity, and computational simulations), with a focus on dynamic and flexibility aspects and to binding analysis. This will provide insights on the currently available RNA therapeutic applications and on the best techniques to evaluate its dynamics and reactivity.

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Section: Experimental Methods For the Study Of Rna Dynamics And Flexi...mentioning

confidence: 99%

An overview of structural approaches to study therapeutic RNAs

Mollica

Cupaioli²,

Rossetti³

et al. 2022

Front. Mol. Biosci.

View full text Add to dashboard Cite

show abstract

“…NMR spectroscopy is an ideal tool for studying chemical and biochemical reactions in real time benefiting from the ease to distinguish different entities based on the NMR chemical-shift values, as well as from the intrinsically quantitative nature of NMR. This allows measurement of reaction kinetics by both, solution- and solid-state NMR . Chemical reactions occurring in the magic-angle spinning (MAS) NMR rotor and followed by real-time NMR have been reported, for instance for battery materials (for a review see ref ), or for mechanochemical transformations (for selected examples see refs − ).…”

Section: Introductionmentioning

confidence: 99%

Initial Primer Synthesis of a DNA Primase Monitored by Real-Time NMR Spectroscopy

Wu,

Zehnder,

Schröder

et al. 2024

J. Am. Chem. Soc.

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Primases are crucial enzymes for DNA replication, as they synthesize a short primer required for initiating DNA replication. We herein present timeresolved nuclear magnetic resonance (NMR) spectroscopy in solution and in the solid state to study the initial dinucleotide formation reaction of archaeal pRN1 primase. Our findings show that the helix-bundle domain (HBD) of pRN1 primase prepares the two substrates and then hands them over to the catalytic domain to initiate the reaction. By using nucleotide triphosphate analogues, the reaction is substantially slowed down, allowing us to study the initial dinucleotide formation in real time. We show that the sedimented protein−DNA complex remains active in the solid-state NMR rotor and that time-resolved 31 P-detected cross-polarization experiments allow monitoring the kinetics of dinucleotide formation. The kinetics in the sedimented protein sample are comparable to those determined by solution-state NMR. Protein conformational changes during primer synthesis are observed in time-resolved 1 H-detected experiments at fast magic-angle spinning frequencies (100 kHz). A significant number of spectral changes cluster in the HBD pointing to the importance of the HBD for positioning the nucleotides and the dinucleotide.

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“…It has also given rise to many new techniques, including multi-nuclear magnetic resonance (multi-NMR), quantitative nuclear magnetic resonance (qNMR), Nuclear Magnetic Resonance Imaging (MRI), Functional MRI (fMRI), Diffusion MRI (dMRI), and Diffusion Tensor Imaging (DTI) [1][2][3][4][5][6][7][8]. These NMR techniques find widespread applications in various fields such as chemistry, biology, agriculture, and medicine [9][10][11][12][13][14]. Due to their ability to analyze metabolites, detect the structures of DNA, RNA, and proteins, and visualize human internal organs/serum without ionizing radiation, these techniques have proved to be versatile and valuable [15][16][17][18][19].…”

Section: Introductionmentioning

confidence: 99%

Insights into Nuclear Magnetic Resonance Data Pre-processing: A Comprehensive Review

Jiang

2024

JDSIS

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Nuclear Magnetic Resonance (NMR) and its derivatives play a pivotal role in molecular analysis across research and clinical domains. However, the intricate nature of NMR data pre-processing, which is integral for accurate analysis, is not easily understood despite the availability of numerous software tools. This comprehensive review aims to unravel the complexities of pre-processing algorithms in both the time and frequency domains. It covers essential steps such as direct current offset removal, eddy current correction, shift and linear prediction, weighting, zero filling, domain transformation, phase error correction, baseline correction, solvent filtering, calibration and alignment, reference deconvolution, binning/bucketing, peak picking, peak fitting/deconvolution, compound identification, integration and quantification, normalization, and transformation. The review uses plain language to enhance accessibility and understanding. By demystifying the algorithms behind these pre-processing steps, we seek to help researchers and practitioners in navigating the nuances of NMR data pre-processing, ultimately fostering better understanding and practical application in molecular analysis.

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

Cited by 7 publications

References 249 publications

An overview of structural approaches to study therapeutic RNAs

An overview of structural approaches to study therapeutic RNAs

Initial Primer Synthesis of a DNA Primase Monitored by Real-Time NMR Spectroscopy

Insights into Nuclear Magnetic Resonance Data Pre-processing: A Comprehensive Review

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