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Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids

Residual dipolar couplings (RDCs) are increasingly used for high-throughput NMR-based structural studies and to provide long-range angular constraints to validate and refine structures of various molecules determined by X-ray crystallography and NMR spectroscopy. RDCs of a given molecule can be meas...

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Autores principales: Krishnarjuna, Bankala, Ravula, Thirupathi, Faison, Edgar M., Tonelli, Marco, Zhang, Qi, Ramamoorthy, Ayyalusamy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9687133/
https://www.ncbi.nlm.nih.gov/pubmed/36358983
http://dx.doi.org/10.3390/biom12111628
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author Krishnarjuna, Bankala
Ravula, Thirupathi
Faison, Edgar M.
Tonelli, Marco
Zhang, Qi
Ramamoorthy, Ayyalusamy
author_facet Krishnarjuna, Bankala
Ravula, Thirupathi
Faison, Edgar M.
Tonelli, Marco
Zhang, Qi
Ramamoorthy, Ayyalusamy
author_sort Krishnarjuna, Bankala
collection PubMed
description Residual dipolar couplings (RDCs) are increasingly used for high-throughput NMR-based structural studies and to provide long-range angular constraints to validate and refine structures of various molecules determined by X-ray crystallography and NMR spectroscopy. RDCs of a given molecule can be measured in an anisotropic environment that aligns in an external magnetic field. Here, we demonstrate the first application of polymer-based nanodiscs for the measurement of RDCs from nucleic acids. Polymer-based nanodiscs prepared using negatively charged SMA-EA polymer and zwitterionic DMPC lipids were characterized by size-exclusion chromatography, (1)H NMR, dynamic light-scattering, and (2)H NMR. The magnetically aligned polymer-nanodiscs were used as an alignment medium to measure RDCs from a (13)C/(15)N-labeled fluoride riboswitch aptamer using 2D ARTSY-HSQC NMR experiments. The results showed that the alignment of nanodiscs is stable for nucleic acids and nanodisc-induced RDCs fit well with the previously determined solution structure of the riboswitch. These results demonstrate that SMA-EA-based lipid-nanodiscs can be used as a stable alignment medium for high-resolution structural and dynamical studies of nucleic acids, and they can also be applicable to study various other biomolecules and small molecules in general.
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spelling pubmed-96871332022-11-25 Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids Krishnarjuna, Bankala Ravula, Thirupathi Faison, Edgar M. Tonelli, Marco Zhang, Qi Ramamoorthy, Ayyalusamy Biomolecules Article Residual dipolar couplings (RDCs) are increasingly used for high-throughput NMR-based structural studies and to provide long-range angular constraints to validate and refine structures of various molecules determined by X-ray crystallography and NMR spectroscopy. RDCs of a given molecule can be measured in an anisotropic environment that aligns in an external magnetic field. Here, we demonstrate the first application of polymer-based nanodiscs for the measurement of RDCs from nucleic acids. Polymer-based nanodiscs prepared using negatively charged SMA-EA polymer and zwitterionic DMPC lipids were characterized by size-exclusion chromatography, (1)H NMR, dynamic light-scattering, and (2)H NMR. The magnetically aligned polymer-nanodiscs were used as an alignment medium to measure RDCs from a (13)C/(15)N-labeled fluoride riboswitch aptamer using 2D ARTSY-HSQC NMR experiments. The results showed that the alignment of nanodiscs is stable for nucleic acids and nanodisc-induced RDCs fit well with the previously determined solution structure of the riboswitch. These results demonstrate that SMA-EA-based lipid-nanodiscs can be used as a stable alignment medium for high-resolution structural and dynamical studies of nucleic acids, and they can also be applicable to study various other biomolecules and small molecules in general. MDPI 2022-11-03 /pmc/articles/PMC9687133/ /pubmed/36358983 http://dx.doi.org/10.3390/biom12111628 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Krishnarjuna, Bankala
Ravula, Thirupathi
Faison, Edgar M.
Tonelli, Marco
Zhang, Qi
Ramamoorthy, Ayyalusamy
Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids
title Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids
title_full Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids
title_fullStr Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids
title_full_unstemmed Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids
title_short Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids
title_sort polymer-nanodiscs as a novel alignment medium for high-resolution nmr-based structural studies of nucleic acids
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9687133/
https://www.ncbi.nlm.nih.gov/pubmed/36358983
http://dx.doi.org/10.3390/biom12111628
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