Literature DB >> 25186910

Development and application of aromatic [(13)C, (1)H] SOFAST-HMQC NMR experiment for nucleic acids.

Bharathwaj Sathyamoorthy1, Janghyun Lee, Isaac Kimsey, Laura R Ganser, Hashim Al-Hashimi.   

Abstract

Higher sensitivity of NMR spectrometers and novel isotopic labeling schemes have ushered the development of rapid data acquisition methodologies, improving the time resolution with which NMR data can be acquired. For nucleic acids, longitudinal relaxation optimization in conjunction with Ernst angle excitation (SOFAST-HMQC) for imino protons, in addition to rendering rapid pulsing, has been demonstrated to yield significant improvements in sensitivity per unit time. Extending such methodology to other spins offers a viable prospect to measure additional chemical shifts, thereby broadening their utilization for various applications. Here, we introduce the 2D [(13)C, (1)H] aromatic SOFAST-HMQC that results in overall sensitivity gain of 1.4- to 1.7-fold relative to the conventional HMQC and can also be extended to yield long-range heteronuclear chemical shifts such as the adenine imino nitrogens N1, N3, N7 and N9. The applications of these experiments range from monitoring real-time biochemical processes, drug/ligand screening, and to collecting data at very low sample concentration and/or in cases where isotopic enrichment cannot be achieved.

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Year:  2014        PMID: 25186910      PMCID: PMC4324173          DOI: 10.1007/s10858-014-9856-9

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  59 in total

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4.  Single-scan multidimensional magnetic resonance.

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5.  Analysis of the contributions of ring current and electric field effects to the chemical shifts of RNA bases.

Authors:  Aleksandr B Sahakyan; Michele Vendruscolo
Journal:  J Phys Chem B       Date:  2013-02-11       Impact factor: 2.991

6.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

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Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

Review 7.  Functional complexity and regulation through RNA dynamics.

Authors:  Elizabeth A Dethoff; Jeetender Chugh; Anthony M Mustoe; Hashim M Al-Hashimi
Journal:  Nature       Date:  2012-02-15       Impact factor: 49.962

8.  Resolution enhanced homonuclear carbon decoupled triple resonance experiments for unambiguous RNA structural characterization.

Authors:  Kwaku T Dayie
Journal:  J Biomol NMR       Date:  2005-06       Impact factor: 2.835

9.  Evaluation of parameters critical for observing nucleic acids inside living Xenopus laevis oocytes by in-cell NMR spectroscopy.

Authors:  Robert Hänsel; Silvie Foldynová-Trantírková; Frank Löhr; Janina Buck; Eva Bongartz; Ernst Bamberg; Harald Schwalbe; Volker Dötsch; Lukás Trantírek
Journal:  J Am Chem Soc       Date:  2009-11-04       Impact factor: 15.419

10.  Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids in solution.

Authors:  Jonathan Farjon; Jérôme Boisbouvier; Paul Schanda; Arthur Pardi; Jean-Pierre Simorre; Bernhard Brutscher
Journal:  J Am Chem Soc       Date:  2009-06-24       Impact factor: 15.419

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  19 in total

Review 1.  RNA Structural Differentiation: Opportunities with Pattern Recognition.

Authors:  Christopher S Eubanks; Amanda E Hargrove
Journal:  Biochemistry       Date:  2018-12-18       Impact factor: 3.162

2.  Robust IR-based detection of stable and fractionally populated G-C+ and A-T Hoogsteen base pairs in duplex DNA.

Authors:  Allison L Stelling; Yu Xu; Huiqing Zhou; Seung H Choi; Mary C Clay; Dawn K Merriman; Hashim M Al-Hashimi
Journal:  FEBS Lett       Date:  2017-06-19       Impact factor: 4.124

3.  Long-Range RNA Structural Information via a Paramagnetically Tagged Reporter Protein.

Authors:  Madeleine Strickland; Jonathan Catazaro; Rohith Rajasekaran; Marie-Paule Strub; Colin O'Hern; Guillermo A Bermejo; Michael F Summers; Jan Marchant; Nico Tjandra
Journal:  J Am Chem Soc       Date:  2019-01-22       Impact factor: 15.419

4.  Characterizing RNA Excited States Using NMR Relaxation Dispersion.

Authors:  Yi Xue; Dawn Kellogg; Isaac J Kimsey; Bharathwaj Sathyamoorthy; Zachary W Stein; Mitchell McBrairty; Hashim M Al-Hashimi
Journal:  Methods Enzymol       Date:  2015-03-25       Impact factor: 1.600

5.  Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales.

Authors:  Dawn K Merriman; Yi Xue; Shan Yang; Isaac J Kimsey; Anisha Shakya; Mary Clay; Hashim M Al-Hashimi
Journal:  Biochemistry       Date:  2016-08-04       Impact factor: 3.162

6.  Probing RNA Conformational Equilibria within the Functional Cellular Context.

Authors:  Laura R Ganser; Chia-Chieh Chu; Hal P Bogerd; Megan L Kelly; Bryan R Cullen; Hashim M Al-Hashimi
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7.  15N and 13C- SOFAST-HMQC editing enhances 3D-NOESY sensitivity in highly deuterated, selectively [1H,13C]-labeled proteins.

Authors:  Paolo Rossi; Youlin Xia; Nandish Khanra; Gianluigi Veglia; Charalampos G Kalodimos
Journal:  J Biomol NMR       Date:  2016-11-23       Impact factor: 2.835

8.  Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.

Authors:  Bharathwaj Sathyamoorthy; Honglue Shi; Huiqing Zhou; Yi Xue; Atul Rangadurai; Dawn K Merriman; Hashim M Al-Hashimi
Journal:  Nucleic Acids Res       Date:  2017-05-19       Impact factor: 16.971

9.  Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes.

Authors:  Isaac J Kimsey; Katja Petzold; Bharathwaj Sathyamoorthy; Zachary W Stein; Hashim M Al-Hashimi
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10.  Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?

Authors:  Atul Rangadurai; Huiqing Zhou; Dawn K Merriman; Nathalie Meiser; Bei Liu; Honglue Shi; Eric S Szymanski; Hashim M Al-Hashimi
Journal:  Nucleic Acids Res       Date:  2018-11-16       Impact factor: 16.971

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