1
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Novakovic M, Kim J, Su XC, Kupče E, Frydman L. Relaxation-Assisted Magnetization Transfer Phenomena for a Sensitivity-Enhanced 2D NMR. Anal Chem 2023; 95:18091-18098. [PMID: 38008904 PMCID: PMC10719887 DOI: 10.1021/acs.analchem.3c03149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/28/2023]
Abstract
2D NOESY and TOCSY play central roles in contemporary NMR. We have recently discussed how solvent-driven exchanges can significantly enhance the sensitivity of such methods when attempting correlations between labile and nonlabile protons. This study explores two scenarios where similar sensitivity enhancements can be achieved in the absence of solvent exchange: the first one involves biomolecular paramagnetic systems, while the other involves small organic molecules in natural abundance. It is shown that, in both cases, the effects introduced by either differential paramagnetic shift and relaxation or by polarization sharing among networks of protons can provide a similar sensitivity boost, as previously discussed for solvent exchange. The origin and potential of the resulting enhancements are analyzed, and experiments that demonstrate them in protein and natural products are exemplified. Limitations and future improvements of these approaches are also briefly discussed.
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Affiliation(s)
- Mihajlo Novakovic
- Departments
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Jihyun Kim
- Departments
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
- Department
of Chemistry Education, Kyungpook National
University, Daegu 41566, Republic of Korea
| | - Xun-Cheng Su
- State
Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - E̅riks Kupče
- Bruker
Ltd., Banner Lane, Coventry CV4 9GH, United Kingdom
| | - Lucio Frydman
- Departments
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
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2
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Wang D, Wang X, Ye F, Zou J, Qu J, Jiang X. An Integrated Amplification-Free Digital CRISPR/Cas-Assisted Assay for Single Molecule Detection of RNA. ACS NANO 2023; 17:7250-7256. [PMID: 37052221 PMCID: PMC10108731 DOI: 10.1021/acsnano.2c10143] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 04/10/2023] [Indexed: 05/09/2023]
Abstract
Conventional nucleic acid detection technologies usually rely on amplification to improve sensitivity, which has drawbacks, such as amplification bias, complicated operation, high requirements for complex instruments, and aerosol pollution. To address these concerns, we developed an integrated assay for the enrichment and single molecule digital detection of nucleic acid based on a CRISPR/Cas13a and microwell array. In our design, magnetic beads capture and concentrate the target from a large volume of sample, which is 100 times larger than reported earlier. The target-induced CRISPR/Cas13a cutting reaction was then dispersed and limited to a million individual femtoliter-sized microwells, thereby enhancing the local signal intensity to achieve single-molecule detection. The limit of this assay for amplification-free detection of SARS-CoV-2 is 2 aM. The implementation of this study will establish a "sample-in-answer-out" single-RNA detection technology without amplification and improve the sensitivity and specificity while shortening the detection time. This research has broad prospects in clinical application.
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Affiliation(s)
- Dou Wang
- Shenzhen Key Laboratory of Smart Healthcare
Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of
Biomedical Engineering, Southern University of Science and
Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen,
Guangdong 518055, P. R. China
| | - Xuedong Wang
- Shenzhen Key Laboratory of Smart Healthcare
Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of
Biomedical Engineering, Southern University of Science and
Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen,
Guangdong 518055, P. R. China
| | - Feidi Ye
- Department of Clinical Laboratory,
Shenzhen Third People’s Hospital, Second Hospital Affiliated to
Southern University of Science and Technology, National Clinical Research Center for
Infectious Diseases, Guangdong, 518055, P. R.
China
| | - Jin Zou
- Department of Clinical Laboratory,
Shenzhen Third People’s Hospital, Second Hospital Affiliated to
Southern University of Science and Technology, National Clinical Research Center for
Infectious Diseases, Guangdong, 518055, P. R.
China
| | - Jiuxin Qu
- Department of Clinical Laboratory,
Shenzhen Third People’s Hospital, Second Hospital Affiliated to
Southern University of Science and Technology, National Clinical Research Center for
Infectious Diseases, Guangdong, 518055, P. R.
China
| | - Xingyu Jiang
- Shenzhen Key Laboratory of Smart Healthcare
Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of
Biomedical Engineering, Southern University of Science and
Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen,
Guangdong 518055, P. R. China
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3
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Duchardt-Ferner E, Ferner J, Fürtig B, Hengesbach M, Richter C, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Schwalbe H. The COVID19-NMR Consortium: A Public Report on the Impact of this New Global Collaboration. Angew Chem Int Ed Engl 2023; 62:e202217171. [PMID: 36748955 DOI: 10.1002/anie.202217171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Indexed: 02/08/2023]
Abstract
The outbreak of COVID-19 in December 2019 required the formation of international consortia for a coordinated scientific effort to understand and combat the virus. In this Viewpoint Article, we discuss how the NMR community has gathered to investigate the genome and proteome of SARS-CoV-2 and tested them for binding to low-molecular-weight binders. External factors including extended lockdowns due to the global pandemic character of the viral infection triggered the transition from locally focused collaborative research conducted within individual research groups to digital exchange formats for immediate discussion of unpublished results and data analysis, sample sharing, and coordinated research between more than 50 groups from 18 countries simultaneously. We discuss key lessons that might pertain after the end of the pandemic and challenges that we need to address.
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Affiliation(s)
- Elke Duchardt-Ferner
- Institute for Biomolecular Sciences, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Andreas Schlundt
- Institute for Biomolecular Sciences, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Julia E Weigand
- Philipps-University Marburg, Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35037, Marburg, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, OX4 2JY, UK
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4
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Grün JT, Kim J, Jayanthi S, Lupulescu A, Kupče ER, Schwalbe H, Frydman L. Identifying and Overcoming Artifacts in 1 H-Based Saturation Transfer NOE NMR Experiments. J Am Chem Soc 2023; 145:6289-6298. [PMID: 36877814 PMCID: PMC10037324 DOI: 10.1021/jacs.2c13087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Magnetization transfer experiments are versatile nuclear magnetic resonance (NMR) tools providing site-specific information. We have recently discussed how saturation magnetization transfer (SMT) experiments could leverage repeated repolarizations arising from exchanges between labile and water protons to enhance connectivities revealed via the nuclear Overhauser effect (NOE). Repeated experience with SMT has shown that a number of artifacts may arise in these experiments, which may confound the information being sought - particularly when seeking small NOEs among closely spaced resonances. One of these pertains to what we refer to as "spill-over" effects, originating from the use of long saturation pulses leading to changes in the signals of proximate peaks. A second, related but in fact different effect, derives from what we describe as NOE "oversaturation", a phenomenon whereby the use of overtly intense RF fields overwhelms the cross-relaxation signature. The origin and ways to avoid these two effects are described. A final source of potential artifact arises in applications where the labile 1Hs of interest are bound to 15N-labeled heteronuclei. SMT's long 1H saturation times will then be usually implemented while under 15N decoupling based on cyclic schemes leading to decoupling sidebands. Although these sidebands usually remain invisible in NMR, they may lead to a very efficient saturation of the main resonance when touched by SMT frequencies. All of these phenomena are herein experimentally demonstrated, and solutions to overcome them are proposed.
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Affiliation(s)
- J Tassilo Grün
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jihyun Kim
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sundaresan Jayanthi
- Department of Physics, Indian Institute of Space Science and Technology, Valiamala, Thiruvananthapuram 695547, Kerala, India
| | - Adonis Lupulescu
- Extreme Light Infrastructure─Nuclear Physics, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, 077125 Bucharest-Măgurele, Romania
| | - E Riks Kupče
- Bruker UK Ltd., Welland House, Westwood Business Park, Coventry CV4 9GH, U.K
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe-University, 60438 Frankfurt/Main, Germany
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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5
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Duchardt‐Ferner E, Ferner J, Fürtig B, Hengesbach M, Richter C, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer‐Bartoschek J, Schwalbe H. Das COVID19‐NMR‐Konsortium: Ein öffentlicher Bericht über den Einfluss dieser neuen globalen Kollaboration. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202217171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- Elke Duchardt‐Ferner
- Institute for Biomolecular Sciences Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt/M. Deutschland
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Andreas Schlundt
- Institute for Biomolecular Sciences Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt/M. Deutschland
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Julia E. Weigand
- Philipps-University Marburg Department of Pharmacy Institute of Pharmaceutical Chemistry Marbacher Weg 6 35037 Marburg Deutschland
| | - Julia Wirmer‐Bartoschek
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
- Instruct-ERIC Oxford House, Parkway Court John Smith Drive Oxford OX4 2JY Großbritannien
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6
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Chen Z, Li X, Huang Y, Cao S, Chen Z, Lin Y. High-resolution NMR spectroscopy for measuring complex samples based on chemical-shift-difference selection. Phys Chem Chem Phys 2023; 25:999-1005. [PMID: 36533435 DOI: 10.1039/d2cp04279g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
NMR spectroscopy serves as an immensely powerful tool for component assignments and molecular structure elucidations. However, proton NMR spectra are generally trapped with spectral congestion caused by limited frequency differences and complex multiplets. 2D NMR can effectively relieve spectral congestion, but its resolution and acquisition efficiency are restricted by the broad spectral bandwidth. Herein, we introduce an NMR method based on chemical-shift-difference selection by chirp excitation to record high-resolution 2D NMR spectra for extracting coupling correlation networks and multiplet structures, suitable for measurements on complex samples. The performance of the proposed method is illustrated in determining diastereotopic methylene protons, small frequency-difference coupled proton pairs of furanose, pyranose and benzene rings. This study is expected to benefit molecular structure elucidation and composition analysis of complex samples in chemistry, biochemistry and metabonomics.
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Affiliation(s)
- Ziqiao Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China.
| | - Xueting Li
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China.
| | - Yuqing Huang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China.
| | - Shuohui Cao
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China.
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China.
| | - Yulan Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China.
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7
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Kim J, Novakovic M, Jayanthi S, Lupulescu A, Kupče Ē, Grün JT, Mertinkus K, Oxenfarth A, Schwalbe H, Frydman L. The Extended Hadamard Transform: Sensitivity-Enhanced NMR Experiments Among Labile and Non-Labile 1 Hs of SARS-CoV-2-derived RNAs. Chemphyschem 2022; 23:e202100704. [PMID: 34968005 PMCID: PMC9015374 DOI: 10.1002/cphc.202100704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/29/2021] [Indexed: 11/09/2022]
Abstract
Hadamard encoded saturation transfer can significantly improve the efficiency of NOE-based NMR correlations from labile protons in proteins, glycans and RNAs, increasing the sensitivity of cross-peaks by an order of magnitude and shortening experimental times by ≥100-fold. These schemes, however, fail when tackling correlations within a pool of labile protons - for instance imino-imino correlations in RNAs or amide-amide correlations in proteins. Here we analyze the origin of the artifacts appearing in these experiments and propose a way to obtain artifact-free correlations both within the labile pool as well as between labile and non-labile 1 Hs, while still enjoying the gains arising from Hadamard encoding and solvent repolarizations. The principles required for implementing what we define as the extended Hadamard scheme are derived, and its clean, artifact-free, sensitivity-enhancing performance is demonstrated on RNA fragments derived from the SARS-CoV-2 genome. Sensitivity gains per unit time approaching an order of magnitude are then achieved in both imino-imino and imino-amino/aromatic protons 2D correlations; similar artifact-free sensitivity gains can be observed when carrying out extended Hadamard encodings of 3D NOESY/HSQC-type experiments. The resulting spectra reveal significantly more correlations than their conventionally acquired counterparts, which can support the spectral assignment and secondary structure determination of structured RNA elements.
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Affiliation(s)
- Jihyun Kim
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Sundaresan Jayanthi
- Department of Physics, Indian Institute of Space Science and Technology, Valiamala, 695 547, Thiruvananthapuram, Kerala, India
| | - Adonis Lupulescu
- "Horia Hulubei" National Institute for Physics and Nuclear Engineering IFIN-HH, 30 Reactorului Street, 077125, Bucharest-Măgurele, Romania
| | - Ēriks Kupče
- Bruker UK, Banner Lane, Coventry, CV4 9GH, UK
| | - J Tassilo Grün
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Klara Mertinkus
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, FrankfurtFrankfurt/Main, Germany
| | - Andreas Oxenfarth
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, FrankfurtFrankfurt/Main, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, FrankfurtFrankfurt/Main, Germany
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
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8
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Bottaro S, Bussi G, Lindorff-Larsen K. Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations. J Am Chem Soc 2021; 143:8333-8343. [PMID: 34039006 PMCID: PMC8188756 DOI: 10.1021/jacs.1c01094] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Indexed: 12/17/2022]
Abstract
The 5' untranslated region (UTR) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome is a conserved, functional and structured genomic region consisting of several RNA stem-loop elements. While the secondary structure of such elements has been determined experimentally, their three-dimensional structures are not known yet. Here, we predict structure and dynamics of five RNA stem loops in the 5'-UTR of SARS-CoV-2 by extensive atomistic molecular dynamics simulations, more than 0.5 ms of aggregate simulation time, in combination with enhanced sampling techniques. We compare simulations with available experimental data, describe the resulting conformational ensembles, and identify the presence of specific structural rearrangements in apical and internal loops that may be functionally relevant. Our atomic-detailed structural predictions reveal a rich dynamics in these RNA molecules, could help the experimental characterization of these systems, and provide putative three-dimensional models for structure-based drug design studies.
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Affiliation(s)
- Sandro Bottaro
- Structural
Biology and NMR Laboratory & Linderstrøm-Lang Centre for
Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Giovanni Bussi
- Scuola
Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory & Linderstrøm-Lang Centre for
Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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9
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Novakovic M, Kupče Ē, Scherf T, Oxenfarth A, Schnieders R, Grün JT, Wirmer-Bartoschek J, Richter C, Schwalbe H, Frydman L. Magnetization Transfer to Enhance NOE Cross-Peaks among Labile Protons: Applications to Imino-Imino Sequential Walks in SARS-CoV-2-Derived RNAs. Angew Chem Int Ed Engl 2021; 60:11884-11891. [PMID: 33683819 PMCID: PMC8251384 DOI: 10.1002/anie.202015948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/14/2021] [Indexed: 11/17/2022]
Abstract
2D NOESY plays a central role in structural NMR spectroscopy. We have recently discussed methods that rely on solvent‐driven exchanges to enhance NOE correlations between exchangeable and non‐exchangeable protons in nucleic acids. Such methods, however, fail when trying to establish connectivities within pools of labile protons. This study introduces an alternative that also enhances NOEs between such labile sites, based on encoding a priori selected peaks by selective saturations. The resulting selective magnetization transfer (SMT) experiment proves particularly useful for enhancing the imino–imino cross‐peaks in RNAs, which is a first step in the NMR resolution of these structures. The origins of these enhancements are discussed, and their potential is demonstrated on RNA fragments derived from the genome of SARS‐CoV‐2, recorded with better sensitivity and an order of magnitude faster than conventional 2D counterparts.
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Affiliation(s)
- Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | | | - Tali Scherf
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, Frankfurt/Main, Germany
| | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, Frankfurt/Main, Germany
| | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, Frankfurt/Main, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, Frankfurt/Main, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, Frankfurt/Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, Frankfurt/Main, Germany
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
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