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Literature DB >> 18807198

Conformational signatures of 13C chemical shifts in RNA ribose.

Oliver Ohlenschläger¹, Sebastian Haumann, Ramadurai Ramachandran, Matthias Görlach.

Abstract

The conformational dependence of (13)C chemical shift values of RNA riboses determined by liquid-state NMR spectroscopy was evaluated using data deposited for RNA structures in the RCSD and BMRB data bases. Results derived support the applicability of the canonical coordinates approach of Rossi and Harbison (J Magn Reson 151:1-8, 2001) in liquid-state NMR to assess the sugar pucker of ribose units in RNA.

Entities: Chemical

Mesh：

Substances：
Carbon Isotopes
RNA
Ribose

Year: 2008 PMID： 18807198 DOI： 10.1007/s10858-008-9271-1

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

9 in total

1. Calculation of 13C chemical shifts in rna nucleosides: structure-13C chemical shift relationships.

Authors: P Rossi; G S Harbison
Journal: J Magn Reson Date: 2001-07 Impact factor: 2.229

Review 2. NMR spectroscopy of RNA.

Authors: Boris Fürtig; Christian Richter; Jens Wöhnert; Harald Schwalbe
Journal: Chembiochem Date: 2003-10-06 Impact factor: 3.164

3. MOLMOL: a program for display and analysis of macromolecular structures.

Authors: R Koradi; M Billeter; K Wüthrich
Journal: J Mol Graph Date: 1996-02

4. Determination of the DNA sugar pucker using 13C NMR spectroscopy.

Authors: R A Santos; P Tang; G S Harbison
Journal: Biochemistry Date: 1989-11-28 Impact factor: 3.162

5. Dependence of 13C NMR chemical shifts on conformations of rna nucleosides and nucleotides.

Authors: M Ebrahimi; P Rossi; C Rogers; G S Harbison
Journal: J Magn Reson Date: 2001-05 Impact factor: 2.229

6. Preparation of 13C and 15N labelled RNAs for heteronuclear multi-dimensional NMR studies.

Authors: E P Nikonowicz; A Sirr; P Legault; F M Jucker; L M Baer; A Pardi
Journal: Nucleic Acids Res Date: 1992-09-11 Impact factor: 16.971

7. Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA.

Authors: R T Batey; M Inada; E Kujawinski; J D Puglisi; J R Williamson
Journal: Nucleic Acids Res Date: 1992-09-11 Impact factor: 16.971

8. Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings.

Authors: Petr Padrta; Richard Stefl; Lukás Králík; Lukás Zídek; Vladimir Sklenár
Journal: J Biomol NMR Date: 2002-09 Impact factor: 2.835

9. The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data.

Authors: D S Wishart; B D Sykes
Journal: J Biomol NMR Date: 1994-03 Impact factor: 2.835

9 in total

11 in total

1. A procedure to validate and correct the 13C chemical shift calibration of RNA datasets.

Authors: Thomas Aeschbacher; Mario Schubert; Frédéric H-T Allain
Journal: J Biomol NMR Date: 2012-01-18 Impact factor: 2.835

2. 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

3. Nucleotide-type chemical shift assignment of the encapsulated 40 kbp dsDNA in intact bacteriophage T7 by MAS solid-state NMR.

Authors: Gili Abramov; Amir Goldbourt
Journal: J Biomol NMR Date: 2014-05-30 Impact factor: 2.835

Review 4. Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R_1ρ relaxation dispersion.

Authors: Atul Rangadurai; Eric S Szymaski; Isaac J Kimsey; Honglue Shi; Hashim M Al-Hashimi
Journal: Prog Nucl Magn Reson Spectrosc Date: 2019-05-11 Impact factor: 9.795

Conformational signatures of 13C chemical shifts in RNA ribose.

1. Calculation of 13C chemical shifts in rna nucleosides: structure-13C chemical shift relationships.

Review 2. NMR spectroscopy of RNA.

3. MOLMOL: a program for display and analysis of macromolecular structures.

4. Determination of the DNA sugar pucker using 13C NMR spectroscopy.

5. Dependence of 13C NMR chemical shifts on conformations of rna nucleosides and nucleotides.

6. Preparation of 13C and 15N labelled RNAs for heteronuclear multi-dimensional NMR studies.

7. Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA.

8. Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings.

9. The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data.

1. A procedure to validate and correct the 13C chemical shift calibration of RNA datasets.

2. Characterizing RNA Excited States Using NMR Relaxation Dispersion.

3. Nucleotide-type chemical shift assignment of the encapsulated 40 kbp dsDNA in intact bacteriophage T7 by MAS solid-state NMR.

Review 4. Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R_1ρ relaxation dispersion.

5. 13C-direct detected NMR experiments for the sequential J-based resonance assignment of RNA oligonucleotides.

6. Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.

7. The structure of the SOLE element of oskar mRNA.

8. DNA structures from phosphate chemical shifts.

9. Database proton NMR chemical shifts for RNA signal assignment and validation.

10. Automated and assisted RNA resonance assignment using NMR chemical shift statistics.

Review 2. NMR spectroscopy of RNA.

Review 4. Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R1ρ relaxation dispersion.

Review 4. Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R_1ρ relaxation dispersion.