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Marchanka, A.

Publications and source records attributed to Marchanka, A..

2 recordsLinked to original sources
bioRxiv2025

Probing site-specific RNA dynamics by solid-state NMR spectroscopy

Knowledge of site-specific dynamics of biomolecules is necessary to understand their specific functions. Solid-state NMR is a uniquely powerful technique that can provide both structural and motional information about complex biomolecules. In recent years, nucleic acids have become increasingly studied by ssNMR, but as yet few RNA or DNA structures are available, with ssNMR-derived dynamics data on RNA rarer still. Here, we report the first systematic ssNMR study of 15N T1 relaxation in RNA using straightforward nucleotide-type-specific and uniform labeling schemes. We observe clear correlation of the measured 15N T1 relaxation time-constants with different structural elements in the RNA molecule, reflecting the distinct characteristics of their underlying motions. We anticipate that this novel approach can be further developed to provide a detailed and comprehensive picture of RNA dynamics in large biomolecular machines.

biophysics↗
bioRxiv2021

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 13C- and 15N-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 1H-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.

biophysics↗