1
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Foster H, Nilsson M, Adams RW, Morris GA. Universally Quantitative Band-Selective Pure Shift NMR Spectroscopy. Anal Chem 2024; 96:9601-9609. [PMID: 38812212 PMCID: PMC11170551 DOI: 10.1021/acs.analchem.4c01199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024]
Abstract
NMR spectroscopy is often described as a quantitative analytical technique. Strictly, only the simple pulse-acquire experiment is universally quantitative, but the poor signal resolution of the 1H NMR pulse-acquie experiment frequently complicates quantitative analysis. Pure shift NMR techniques provide higher resolution, by reducing signal overlap, but they are susceptible to a variety of sources of site-dependent signal loss. Here, we introduce a new method that corrects for signal loss from such sources in band-selective pure shift NMR experiments, by performing different numbers of iterations of the same pulse sequence elements before acquisition to allow extrapolation back to the loss-free signal. We apply this method to both interferogram and semi-realtime acquisition modes, obtaining integrals within 1% of those acquired from a pulse-acquire experiment for a three-component mixture.
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Affiliation(s)
- Howard
M. Foster
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Mathias Nilsson
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Ralph W. Adams
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Gareth A. Morris
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
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2
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Dayie TK, Olenginski LT, Taiwo KM. Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs. Chem Rev 2022; 122:9357-9394. [PMID: 35442658 PMCID: PMC9136934 DOI: 10.1021/acs.chemrev.1c00845] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 02/07/2023]
Abstract
RNA is central to the proper function of cellular processes important for life on earth and implicated in various medical dysfunctions. Yet, RNA structural biology lags significantly behind that of proteins, limiting mechanistic understanding of RNA chemical biology. Fortunately, solution NMR spectroscopy can probe the structural dynamics of RNA in solution at atomic resolution, opening the door to their functional understanding. However, NMR analysis of RNA, with only four unique ribonucleotide building blocks, suffers from spectral crowding and broad linewidths, especially as RNAs grow in size. One effective strategy to overcome these challenges is to introduce NMR-active stable isotopes into RNA. However, traditional uniform labeling methods introduce scalar and dipolar couplings that complicate the implementation and analysis of NMR measurements. This challenge can be circumvented with selective isotope labeling. In this review, we outline the development of labeling technologies and their application to study biologically relevant RNAs and their complexes ranging in size from 5 to 300 kDa by NMR spectroscopy.
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Affiliation(s)
- Theodore K. Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Lukasz T. Olenginski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Kehinde M. Taiwo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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3
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Dubey A, Stoyanov N, Viennet T, Chhabra S, Elter S, Borggräfe J, Viegas A, Nowak RP, Burdzhiev N, Petrov O, Fischer ES, Etzkorn M, Gelev V, Arthanari H. Lokale Deuterierung ermöglicht NMR‐Messung von Methylgruppen in Proteinen aus eukaryotischen und Zell‐freien Expressionssystemen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Abhinav Dubey
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Nikolay Stoyanov
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Thibault Viennet
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Sandeep Chhabra
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Shantha Elter
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Jan Borggräfe
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Aldino Viegas
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Radosław P. Nowak
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Nikola Burdzhiev
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Ognyan Petrov
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Eric S. Fischer
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Manuel Etzkorn
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Vladimir Gelev
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Haribabu Arthanari
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
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4
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Dubey A, Stoyanov N, Viennet T, Chhabra S, Elter S, Borggräfe J, Viegas A, Nowak RP, Burdzhiev N, Petrov O, Fischer ES, Etzkorn M, Gelev V, Arthanari H. Local Deuteration Enables NMR Observation of Methyl Groups in Proteins from Eukaryotic and Cell-Free Expression Systems. Angew Chem Int Ed Engl 2021; 60:13783-13787. [PMID: 33768661 PMCID: PMC8251921 DOI: 10.1002/anie.202016070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/22/2021] [Indexed: 01/13/2023]
Abstract
Therapeutically relevant proteins such as GPCRs, antibodies and kinases face clear limitations in NMR studies due to the challenges in site-specific isotope labeling and deuteration in eukaryotic expression systems. Here we describe an efficient and simple method to observe the methyl groups of leucine residues in proteins expressed in bacterial, eukaryotic or cell-free expression systems without modification of the expression protocol. The method relies on simple stereo-selective 13 C-labeling and deuteration of leucine that alleviates the need for additional deuteration of the protein. The spectroscopic benefits of "local" deuteration are examined in detail through Forbidden Coherence Transfer (FCT) experiments and simulations. The utility of this labeling method is demonstrated in the cell-free synthesis of bacteriorhodopsin and in the insect-cell expression of the RRM2 domain of human RBM39.
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Affiliation(s)
- Abhinav Dubey
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Nikolay Stoyanov
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Thibault Viennet
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Sandeep Chhabra
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Shantha Elter
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Jan Borggräfe
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Aldino Viegas
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Radosław P. Nowak
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Nikola Burdzhiev
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Ognyan Petrov
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Eric S. Fischer
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Manuel Etzkorn
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Vladimir Gelev
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Haribabu Arthanari
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
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5
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Kiraly P, Kern N, Plesniak MP, Nilsson M, Procter DJ, Morris GA, Adams RW. Single-Scan Selective Excitation of Individual NMR Signals in Overlapping Multiplets. Angew Chem Int Ed Engl 2021; 60:666-669. [PMID: 32965750 PMCID: PMC7839668 DOI: 10.1002/anie.202011642] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/17/2020] [Indexed: 11/08/2022]
Abstract
2D NMR is an immensely powerful structural tool but it is time-consuming. Targeting individual chemical groups by selective excitation in a 1D experiment can give the information required far more quickly. A major problem, however, is that proton NMR spectra are often extensively overlapped, so that in practice only a minority of sites can be selectively excited. Here we overcome that problem using a fast, single-scan method that allows selective excitation of the signals of a single proton multiplet even where it is severely overlapped by other multiplets. The advantages of the method are illustrated in a selective 1D NOESY experiment, the most efficient way to determine relative configuration unambiguously by NMR. The new approach presented here has the potential to broaden significantly the applicability of selective excitation and unlock its real potential for many other experiments.
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Affiliation(s)
- Peter Kiraly
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Nicolas Kern
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Mateusz P. Plesniak
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Mathias Nilsson
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - David J. Procter
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Gareth A. Morris
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Ralph W. Adams
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
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6
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Kiraly P, Kern N, Plesniak MP, Nilsson M, Procter DJ, Morris GA, Adams RW. Single‐Scan Selective Excitation of Individual NMR Signals in Overlapping Multiplets. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Peter Kiraly
- Department of Chemistry University of Manchester Oxford Road Manchester M13 9PL UK
| | - Nicolas Kern
- Department of Chemistry University of Manchester Oxford Road Manchester M13 9PL UK
| | - Mateusz P. Plesniak
- Department of Chemistry University of Manchester Oxford Road Manchester M13 9PL UK
| | - Mathias Nilsson
- Department of Chemistry University of Manchester Oxford Road Manchester M13 9PL UK
| | - David J. Procter
- Department of Chemistry University of Manchester Oxford Road Manchester M13 9PL UK
| | - Gareth A. Morris
- Department of Chemistry University of Manchester Oxford Road Manchester M13 9PL UK
| | - Ralph W. Adams
- Department of Chemistry University of Manchester Oxford Road Manchester M13 9PL UK
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7
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Rao Kakita VM, Joshi MV, Hosur RV. G-SERF Editing in Two-Dimensional Pure-Shift Total Correlation Spectroscopy: Scalar Coupling Measurements for a Group of Spins in Organic Molecules. Chemphyschem 2019; 20:1559-1566. [PMID: 30997947 DOI: 10.1002/cphc.201900174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/13/2019] [Indexed: 11/10/2022]
Abstract
A novel G-SERF-PSYCHE-TOCSY (gradient encoded selective refocusing in pure shift yielded by chirp excitation version of total correlation spectroscopy) NMR pulse scheme has been proposed, which produces TOCSY chemical shift correlations, on one hand, and scalar coupling values for the spins scalarly coupled to irradiated resonances, by showing them as doublets along the indirect dimension, on the other. Therefore, recording such an experiment, for a group of spins with overlapping chemical shifts, in organic molecules can adequately provide scalar coupling information in a G-SERF manner along the indirect dimensions, and they can be assigned to particular spin pairs. Such COSY chemical shift correlations (which appear as doublets for the scalarly coupled spins) can be readily discriminated from the TOCSY peaks (which do not show such splitting) in the G-SERF-PSYCHE-TOCSY spectrum.
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Affiliation(s)
- Veera Mohana Rao Kakita
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz, Mumbai, 400 098, India
| | - Mamata V Joshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), 1-Homi Bhabha Road, Colaba, Mumbai, 400 005, India
| | - Ramakrishna V Hosur
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Santacruz, Mumbai, 400 098, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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8
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Abstract
Broadband homodecoupling techniques in NMR, also known as "pure shift" methods, aim to enhance spectral resolution by suppressing the effects of homonuclear coupling interactions to turn multiplet signals into singlets. Such techniques typically work by selecting a subset of "active" nuclear spins to observe, and selectively inverting the remaining, "passive", spins to reverse the effects of coupling. Pure Shift Yielded by Chirp Excitation (PSYCHE) is one such method; it is relatively recent, but has already been successfully implemented in a range of different NMR experiments. Paradoxically, PSYCHE is one of the trickiest of pure shift NMR techniques to understand but one of the easiest to use. Here we offer some insights into theoretical and practical aspects of the method, and into the effects and importance of the experimental parameters. Some recent improvements that enhance the spectral purity of PSYCHE spectra will be presented, and some experimental frameworks, including examples in 1D and 2D NMR spectroscopy, for the implementation of PSYCHE will be introduced.
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Affiliation(s)
| | - Gareth A Morris
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Mathias Nilsson
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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9
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Huang Y, Cao S, Yang Y, Cai S, Zhan H, Tan C, Lin L, Zhang Z, Chen Z. Ultrahigh-Resolution NMR Spectroscopy for Rapid Chemical and Biological Applications in Inhomogeneous Magnetic Fields. Anal Chem 2017; 89:7115-7122. [DOI: 10.1021/acs.analchem.7b01036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yuqing Huang
- Department of Electronic
Science, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Shuohui Cao
- Department of Electronic
Science, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Yu Yang
- Department of Electronic
Science, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Shuhui Cai
- Department of Electronic
Science, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Haolin Zhan
- Department of Electronic
Science, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Chunhua Tan
- Department of Electronic
Science, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Liangjie Lin
- Department of Electronic
Science, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhiyong Zhang
- Department of Electronic
Science, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhong Chen
- Department of Electronic
Science, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
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10
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Castañar L. Pure shift 1 H NMR: what is next? MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:47-53. [PMID: 27761957 DOI: 10.1002/mrc.4545] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/14/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
Currently, pure shift nuclear magnetic resonance (NMR) is an area of high interest. The aim of this contribution is to describe briefly how this technique has evolved, where it is now and what could be the next challenges in the amazing adventure of the development and application of pure shift NMR experiments. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Laura Castañar
- School of Chemistry, University of Manchester, Manchester, UK
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11
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Kakita VMR, Hosur RV. Non-Uniform-Sampling Ultrahigh Resolution TOCSY NMR: Analysis of Complex Mixtures at Microgram Levels. Chemphyschem 2016; 17:2304-8. [DOI: 10.1002/cphc.201600255] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Veera M. R. Kakita
- UM-DAE Centre for Excellence in Basic Sciences; Mumbai University Campus, Kalina, Santa Cruz Mumbai 400 098 India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences; Mumbai University Campus, Kalina, Santa Cruz Mumbai 400 098 India
- Department of Chemical Sciences; Tata Institute of Fundamental Research (TIFR); 1-Homi Bhabha Road, Colaba Mumbai 400 005 India
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12
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Glanzer S, Zangger K. Directly decoupled diffusion-ordered NMR spectroscopy for the analysis of compound mixtures. Chemistry 2014; 20:11171-5. [PMID: 25059845 PMCID: PMC4497316 DOI: 10.1002/chem.201402920] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Indexed: 11/06/2022]
Abstract
For the analysis of compound mixtures by NMR spectroscopy, it is important to assign the different peaks to the individual constituents. Diffusion-ordered spectroscopy (DOSY) is often used for the separation of signals based on their self-diffusion coefficient. However, this method often fails in the case of signal overlap, which is a particular problem for (1)H-detected DOSY spectra. Herein, an approach that allows the acquisition of homonuclear broadband-decoupled DOSY spectra without the introduction of an additional decoupling dimension, by instant decoupling during acquisition, is presented. It was demonstrated on a mixture of six alcohols, and the investigation of the binding of a dodecapeptide to membrane mimetics.
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Affiliation(s)
- Simon Glanzer
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of GrazHeinrichstrasse 28, A-8010 Graz (Austria)
| | - Klaus Zangger
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of GrazHeinrichstrasse 28, A-8010 Graz (Austria)
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13
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Meyer NH, Zangger K. Simplifying proton NMR spectra by instant homonuclear broadband decoupling. Angew Chem Int Ed Engl 2013; 52:7143-6. [PMID: 23733677 PMCID: PMC3790959 DOI: 10.1002/anie.201300129] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/27/2013] [Indexed: 11/28/2022]
Affiliation(s)
- N Helge Meyer
- Institut für Chemie/Organische und Bioorganische Chemie, Karl-Franzens Universität Graz, Heinrichstrasse 28, 8010 Graz, Austria
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14
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Dayie KT. Resolution enhanced homonuclear carbon decoupled triple resonance experiments for unambiguous RNA structural characterization. JOURNAL OF BIOMOLECULAR NMR 2005; 32:129-39. [PMID: 16034664 DOI: 10.1007/s10858-005-5093-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2005] [Accepted: 03/21/2005] [Indexed: 05/03/2023]
Abstract
Large RNAs (>30 nucleotides) suffer from extensive resonance overlap that can seriously hamper unambiguous structural characterization. Here we present a set of 3D multinuclear NMR experiments with improved and optimized resolution and sensitivity for aiding with the assignment of RNA molecules. In all these experiments strong base and ribose carbon-carbon couplings are eliminated by homonuclear band-selective decoupling, leading to improved signal to noise and resolution of the C5, C6, and C1' carbon resonances. This decoupling scheme is applied to base-type selective 13C-edited NOESY, 13C-edited TOCSY (HCCH, CCH), HCCNH, and ribose H1C1C2 experiments. The 3D implementation of the HCCNH experiment with both carbon and nitrogen evolution enables direct correlation of 13C and 15N resonances at different proton resonant frequencies. The advantages of the new experiments are demonstrated on a 36 nucleotides hairpin RNA from domain 5 (D5) of the group II intron Pylaiella littoralis using an abbreviated assignment strategy. These four experiments provided additional separation for regions of the RNA that have overlapped chemical shift resonances, and enabled the assignment of critical D5 bulge nucleotides that could not be assigned using current experimental schemes.
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Affiliation(s)
- Kwaku T Dayie
- Department of Molecular Genetics and Program in Structural Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA.
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15
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Xia Y, Legge G, Jun KY, Qi Y, Lee H, Gao X. IP-COSY, a totally in-phase and sensitive COSY experiment. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2005; 43:372-379. [PMID: 15706609 DOI: 10.1002/mrc.1558] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The IP-COSY experiment presented in this paper gives an in-phase spectral presentation in both the F(1) and F(2) dimensions by a combined use of a constant evolution time (CT) in t(1) and a symmetrical refocusing period before t(2). Compared with DQF-COSY and CT-COSY, IP-COSY further alleviates the effect of signal reduction due to a small ratio p (= J/linewidth), showing (1) improved lineshape and cross-peak definition and (2) especially enhancement in signals of the peaks of small active J coupling constant and the peaks of broader linewidth. A new strategy was adopted to eliminate or reduce effectively artifactual peaks by adding a 0.1-0.2 ms variation to the time delays of the CT period used for each scan of the FID in IP-COSY and CT-COSY. (3)J(H,H) coupling constants of larger than 4 Hz in the fingerprint region of peptides can be directly derived from the separation of doublets. IP-COSY cross peaks are stronger than those in DQF-COSY by 4-20-fold for tested peptides and oligonucleotides (MW < 8 kDa) with acquisition and processing parameters used in the work, and they are easier to identify than those in CT-COSY. The overall improvement in IP-COSY should make the detection/autodetection of the COSY cross peaks and the measurements of the various coupling constants more easily achieved, providing valuable information for the structure elucidation of peptides/small proteins and oligonucleotides.
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Affiliation(s)
- Youlin Xia
- Department of Chemistry, University of Houston, Houston, Texas 77004-5003, USA
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Li N, Yeung HN. Homonuclear broad-band-decoupled chemical shift imaging by singular value decomposition with optimization. IEEE TRANSACTIONS ON MEDICAL IMAGING 1993; 12:342-349. [PMID: 18218424 DOI: 10.1109/42.232265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The conventional viewpoint of localized NMR spectroscopy is to acquire spectral information through time-domain data, while leaving spatial information to phase encoding by incremental magnetic field gradients. A second viewpoint, much less frequently used, places the emphasis on the acquisition of spatially well-resolved images by conventional means, leaving the chemical shift segregation through phase encoding in the incremental t(1) period (in a 2-DNMR parlance). The feasibility and practicality of the second viewpoint are demonstrated by implementation of a modified version of the SLIM technique, which was originally designed for the first viewpoint, using simulated and real phantom data with optimization of the t(1)-encoding parameters.
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Affiliation(s)
- N Li
- Michigan Univ., Ann Arbor, MI
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