Literature DB >> 10677827

Determination of sugar conformation in large RNA oligonucleotides from analysis of dipole-dipole cross correlated relaxation by solution NMR spectroscopy.

C Richter1, C Griesinger, I Felli, P T Cole, G Varani, H Schwalbe.   

Abstract

A new experiment, the forward directed quantitative gamma-HCCH-TOCSY for the measurement of the conformation of the five-membered ribosyl unit in RNA oligonucleotides, is presented. The experiment relies on quantification of cross peak intensities caused by evolution of CH, CH-dipole-dipole cross correlated relaxation in non-evolution periods and the resolution enhancement obtainable in forward directed HCC-TOCSY transfer. Cross correlated relaxation rates are interpreted to reveal the sugar conformation of 22 out of 25 nucleotides in an isotopically labelled 25-mer RNA. The results obtained with this new method are in agreement with the conformational analysis derived from 3J(H,H) coupling constants.

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Year:  1999        PMID： 10677827     DOI： 10.1023/a:1008319130714

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


  14 in total

1.  Directed TOCSY, a method for selection of directed correlations by optimal combinations of isotropic and longitudinal mixing.

Authors:  S J Glaser; H Schwalbe; J P Marino; C Griesinger
Journal:  J Magn Reson B       Date:  1996-08

2.  Direct measurement of angles between bond vectors in high-resolution NMR.

Authors:  B Reif; M Hennig; C Griesinger
Journal:  Science       Date:  1997-05-23       Impact factor: 47.728

3.  A study of protein side-chain dynamics from new 2H auto-correlation and 13C cross-correlation NMR experiments: application to the N-terminal SH3 domain from drk.

Authors:  D Yang; A Mittermaier; Y K Mok; L E Kay
Journal:  J Mol Biol       Date:  1998-03-13       Impact factor: 5.469

4.  Determination of a complete set of coupling constants in 13C-labeled oligonucleotides.

Authors:  H Schwalbe; J P Marino; G C King; R Wechselberger; W Bermel; C Griesinger
Journal:  J Biomol NMR       Date:  1994-09       Impact factor: 2.835

5.  Determination of sugar conformations by NMR in larger DNA duplexes using both dipolar and scalar data: application to d(CATGTGACGTCACATG)2.

Authors:  M R Conte; C J Bauer; A N Lane
Journal:  J Biomol NMR       Date:  1996-05       Impact factor: 2.835

6.  Quantitative investigation of dipole-CSA cross-correlated relaxation by ZQ/DQ spectroscopy.

Authors:  B Brutscher; N R Skrynnikov; T Bremi; R BrYschweiler; R R Ernst
Journal:  J Magn Reson       Date:  1998-02       Impact factor: 2.229

7.  Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible.

Authors:  G Barbato; M Ikura; L E Kay; R W Pastor; A Bax
Journal:  Biochemistry       Date:  1992-06-16       Impact factor: 3.162

8.  New methylene specific experiments for the measurement of scalar spin-spin coupling constants between protons attached to 13C.

Authors:  T Carlomagno; H Schwalbe; A Rexroth; O W Sorensen; C Griesinger
Journal:  J Magn Reson       Date:  1998-11       Impact factor: 2.229

9.  Solution structure of calcium-free calmodulin.

Authors:  H Kuboniwa; N Tjandra; S Grzesiek; H Ren; C B Klee; A Bax
Journal:  Nat Struct Biol       Date:  1995-09

10.  Rotational dynamics of calcium-free calmodulin studied by 15N-NMR relaxation measurements.

Authors:  N Tjandra; H Kuboniwa; H Ren; A Bax
Journal:  Eur J Biochem       Date:  1995-06-15
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  10 in total

1.  Measurement of 2J(H,C)- and 3J(H,C)-coupling constants by alpha/beta selective HC(C)H-TOCSY.

Authors:  E Duchardt; C Richter; B Reif; S J Glaser; J W Engels; C Griesinger; H Schwalbe
Journal:  J Biomol NMR       Date:  2001-10       Impact factor: 2.835

2.  Similarities between intra- and intermolecular hydrogen bonds in RNA kissing complexes found by means of cross-correlated relaxation.

Authors:  Jens Dittmer; Chul-Hyun Kim; Geoffrey Bodenhausen
Journal:  J Biomol NMR       Date:  2003-07       Impact factor: 2.835

3.  Quantitative gamma-HCNCH: determination of the glycosidic torsion angle chi in RNA oligonucleotides from the analysis of CH dipolar cross-correlated relaxation by solution NMR spectroscopy.

Authors:  Jörg Rinnenthal; Christian Richter; Jan Ferner; Elke Duchardt; Harald Schwalbe
Journal:  J Biomol NMR       Date:  2007-07-20       Impact factor: 2.835

4.  Determination of 13C CSA tensors: extension of the model-independent approach to an RNA kissing complex undergoing anisotropic rotational diffusion in solution.

Authors:  Sapna Ravindranathan; Chul-Hyun Kim; Geoffrey Bodenhausen
Journal:  J Biomol NMR       Date:  2005-11       Impact factor: 2.835

5.  Automated NMR determination of protein backbone dihedral angles from cross-correlated spin relaxation.

Authors:  Karin Kloiber; Wolfgang Schüler; Robert Konrat
Journal:  J Biomol NMR       Date:  2002-04       Impact factor: 2.835

6.  Probing slow backbone dynamics in proteins using TROSY-based experiments to detect cross-correlated time-modulation of isotropic chemical shifts.

Authors:  Ananya Majumdar; Ranajeet Ghose
Journal:  J Biomol NMR       Date:  2004-03       Impact factor: 2.835

7.  Time-resolved structural analysis of an RNA-cleaving DNA catalyst.

Authors:  Jan Borggräfe; Julian Victor; Hannah Rosenbach; Aldino Viegas; Christoph G W Gertzen; Christine Wuebben; Helena Kovacs; Mohanraj Gopalswamy; Detlev Riesner; Gerhard Steger; Olav Schiemann; Holger Gohlke; Ingrid Span; Manuel Etzkorn
Journal:  Nature       Date:  2021-12-23       Impact factor: 49.962

Review 8.  Distance-independent Cross-correlated Relaxation and Isotropic Chemical Shift Modulation in Protein Dynamics Studies.

Authors:  Beat Vögeli; Liliya Vugmeyster
Journal:  Chemphyschem       Date:  2018-09-03       Impact factor: 3.520

9.  Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics.

Authors:  David E Condon; Scott D Kennedy; Brendan C Mort; Ryszard Kierzek; Ilyas Yildirim; Douglas H Turner
Journal:  J Chem Theory Comput       Date:  2015-04-16       Impact factor: 6.006

10.  High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA.

Authors:  Senada Nozinovic; Boris Fürtig; Hendrik R A Jonker; Christian Richter; Harald Schwalbe
Journal:  Nucleic Acids Res       Date:  2009-11-11       Impact factor: 16.971
  10 in total

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