Literature DB >> 23946052

Efficient detection of hydrogen bonds in dynamic regions of RNA by sensitivity-optimized NMR pulse sequences.

Andre Dallmann1, Bernd Simon, Malgorzata M Duszczyk, Hamed Kooshapur, Arthur Pardi, Wolfgang Bermel, Michael Sattler.   

Abstract

Improved Sensitivity: Efficient NMR experiments are presented for determining the secondary structure in large and dynamic RNAs using J-couplings across hydrogen bonds. The experiments provide up to eight-fold improved sensitivity and thus enable detection of base pairs in dynamic regions even in large RNAs.
Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Entities:  

Keywords:  NMR spectroscopy; RNA dynamics; RNA secondary structure; base pairs; hydrogen bonds

Mesh：

Substances：

Year:  2013        PMID： 23946052      PMCID： PMC3882076          DOI： 10.1002/anie.201304391

Source DB:  PubMed          Journal:  Angew Chem Int Ed Engl        ISSN： 1433-7851            Impact factor:   15.336


  29 in total

1.  Calculating nucleic acid secondary structure.

Authors:  M Zuker
Journal:  Curr Opin Struct Biol       Date:  2000-06       Impact factor: 6.809

Review 2.  Identifying hydrogen bond alignments in multistranded DNA architectures by NMR.

Authors:  Ananya Majumdar; Dinshaw J Patel
Journal:  Acc Chem Res       Date:  2002-01       Impact factor: 22.384

Review 3.  Scalar couplings across hydrogen bonds.

Authors:  S Grzesiek; F Cordier; A J Dingley
Journal:  Methods Enzymol       Date:  2001       Impact factor: 1.600

4.  Dynamic effects on j-couplings across hydrogen bonds in proteins.

Authors:  Phineus R L Markwick; Remco Sprangers; Michael Sattler
Journal:  J Am Chem Soc       Date:  2003-01-22       Impact factor: 15.419

5.  Characterization of the hydrogen bond network in guanosine quartets by internucleotide 3hJ(NC)' and 2hJ(NN) scalar couplings.

Authors:  A J Dingley; J E Masse; J Feigon; S Grzesiek
Journal:  J Biomol NMR       Date:  2000-04       Impact factor: 2.835

6.  1H-1H correlations across N-H...N hydrogen bonds in nucleic acids.

Authors:  A Majumdar; Y Gosser; D J Patel
Journal:  J Biomol NMR       Date:  2001-12       Impact factor: 2.835

7.  Pulse sequences for detection of NH2...N hydrogen bonds in sheared G . A mismatches via remote, non-exchangeable protons.

Authors:  A Majumdar; A Kettani; E Skripkin; D J Patel
Journal:  J Biomol NMR       Date:  2001-02       Impact factor: 2.835

8.  Observation of internucleotide NH...N hydrogen bonds in the absence of directly detectable protons.

Authors:  A Majumdar; A Kettani; E Skripkin; D J Patel
Journal:  J Biomol NMR       Date:  1999-11       Impact factor: 2.835

Review 9.  Modular regulatory principles of large non-coding RNAs.

Authors:  Mitchell Guttman; John L Rinn
Journal:  Nature       Date:  2012-02-15       Impact factor: 49.962

10.  Observation of H-bond mediated 3hJH2H3 coupling constants across Watson-Crick AU base pairs in RNA.

Authors:  Burkhard Luy; Uwe Richter; Eric S DeJong; Ole W Sørensen; John P Marino
Journal:  J Biomol NMR       Date:  2002-10       Impact factor: 2.835
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  12 in total

1.  Direct ¹³C-detected NMR experiments for mapping and characterization of hydrogen bonds in RNA.

Authors:  Boris Fürtig; Robbin Schnieders; Christian Richter; Heidi Zetzsche; Sara Keyhani; Christina Helmling; Helena Kovacs; Harald Schwalbe
Journal:  J Biomol NMR       Date:  2016-02-06       Impact factor: 2.835

2.  NMR experiments for the rapid identification of P=O···H-X type hydrogen bonds in nucleic acids.

Authors:  Elke Duchardt-Ferner; Jens Wöhnert
Journal:  J Biomol NMR       Date:  2017-10-14       Impact factor: 2.835

Review 3.  Applications of NMR to structure determination of RNAs large and small.

Authors:  Ravi P Barnwal; Fan Yang; Gabriele Varani
Journal:  Arch Biochem Biophys       Date:  2017-06-16       Impact factor: 4.013

4.  Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1.

Authors:  Alisha N Jones; Ekaterina Tikhaia; André Mourão; Michael Sattler
Journal:  Nucleic Acids Res       Date:  2022-02-28       Impact factor: 16.971

5.  Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach.

Authors:  Kaiming Zhang; Sarah C Keane; Zhaoming Su; Rossitza N Irobalieva; Muyuan Chen; Verna Van; Carly A Sciandra; Jan Marchant; Xiao Heng; Michael F Schmid; David A Case; Steven J Ludtke; Michael F Summers; Wah Chiu
Journal:  Structure       Date:  2018-02-02       Impact factor: 5.006

6.  Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine.

Authors:  Elke Duchardt-Ferner; Michael Juen; Benjamin Bourgeois; Tobias Madl; Christoph Kreutz; Oliver Ohlenschläger; Jens Wöhnert
Journal:  Nucleic Acids Res       Date:  2020-01-24       Impact factor: 16.971

7.  The synthesis of 15N(7)-Hoogsteen face-labeled adenosine phosphoramidite for solid-phase RNA synthesis.

Authors:  Sandro Neuner; Christoph Kreutz; Ronald Micura
Journal:  Monatsh Chem       Date:  2016-12-08       Impact factor: 1.451

8.  Structural basis for terminal loop recognition and stimulation of pri-miRNA-18a processing by hnRNP A1.

Authors:  Hamed Kooshapur; Nila Roy Choudhury; Bernd Simon; Max Mühlbauer; Alexander Jussupow; Noemi Fernandez; Alisha N Jones; Andre Dallmann; Frank Gabel; Carlo Camilloni; Gracjan Michlewski; Javier F Caceres; Michael Sattler
Journal:  Nat Commun       Date:  2018-06-26       Impact factor: 14.919

9.  The "Speedy" Synthesis of Atom-Specific (15)N Imino/Amido-Labeled RNA.

Authors:  Sandro Neuner; Tobias Santner; Christoph Kreutz; Ronald Micura
Journal:  Chemistry       Date:  2015-06-17       Impact factor: 5.236

10.  The structure of the SAM/SAH-binding riboswitch.

Authors:  A Katharina Weickhmann; Heiko Keller; Jan P Wurm; Elisabeth Strebitzer; Michael A Juen; Johannes Kremser; Zasha Weinberg; Christoph Kreutz; Elke Duchardt-Ferner; Jens Wöhnert
Journal:  Nucleic Acids Res       Date:  2019-03-18       Impact factor: 16.971
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