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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-11-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/12/11/1628 |
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| author | Bankala Krishnarjuna Thirupathi Ravula Edgar M. Faison Marco Tonelli Qi Zhang Ayyalusamy Ramamoorthy |
| author_facet | Bankala Krishnarjuna Thirupathi Ravula Edgar M. Faison Marco Tonelli Qi Zhang Ayyalusamy Ramamoorthy |
| author_sort | Bankala Krishnarjuna |
| collection | DOAJ |
| 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, <sup>1</sup>H NMR, dynamic light-scattering, and <sup>2</sup>H NMR. The magnetically aligned polymer-nanodiscs were used as an alignment medium to measure RDCs from a <sup>13</sup>C/<sup>15</sup>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. |
| first_indexed | 2024-03-09T19:14:41Z |
| format | Article |
| id | doaj.art-ec8eb75b673b4c218dec2efe16460e36 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-09T19:14:41Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-ec8eb75b673b4c218dec2efe16460e362023-11-24T03:53:45ZengMDPI AGBiomolecules2218-273X2022-11-011211162810.3390/biom12111628Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic AcidsBankala Krishnarjuna0Thirupathi Ravula1Edgar M. Faison2Marco Tonelli3Qi Zhang4Ayyalusamy Ramamoorthy5Biophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USABiophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USADepartment of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USANational Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USADepartment of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USABiophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USAResidual 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, <sup>1</sup>H NMR, dynamic light-scattering, and <sup>2</sup>H NMR. The magnetically aligned polymer-nanodiscs were used as an alignment medium to measure RDCs from a <sup>13</sup>C/<sup>15</sup>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.https://www.mdpi.com/2218-273X/12/11/1628nanodiscsNMRmagnetic alignmentRNAresidual dipolar couplings |
| spellingShingle | Bankala Krishnarjuna Thirupathi Ravula Edgar M. Faison Marco Tonelli Qi Zhang Ayyalusamy Ramamoorthy Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids Biomolecules nanodiscs NMR magnetic alignment RNA residual dipolar couplings |
| 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 | nanodiscs NMR magnetic alignment RNA residual dipolar couplings |
| url | https://www.mdpi.com/2218-273X/12/11/1628 |
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