BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 18593

Title: Solution Structure of a RNA Duplex Containing a 2'-O-Pivaloyloxymethyl Modification   PubMed: 23455628

Authors: Baraguey, Carine

Citation: Baraguey, Carine; Lescrinier, Eveline; Lavergne, Thomas; Debart, Francoise; Herdewijn, Piet; Vasseur, Jean-Jacques. "The biolabile 2'-O-pivaloyloxymethyl modification in an RNA helix: an NMR solution structure"  Org. Biomol. Chem. 11, 2638-2647 (2013).

Assembly members:
modified_strand, polymer, 9 residues, 2499.596 Da.
non-modified_complementary_strand, polymer, 9 residues, 2885.813 Da.

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
modified_strand: CGCXACGCT
non-modified_complementary_strand: GCGUAGCGT

Data sets:
Data typeCount
1H chemical shifts178

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA/RNA (5'-R(CP*GP*CP*(UPV)*AP*CP*GP*C)-D(P*T)-3')1
2DNA/RNA (5'-R(GP*CP*GP*UP*AP*CP*GP*C)-D(P*T)-3')2

Entities:

Entity 1, DNA/RNA (5'-R(CP*GP*CP*(UPV)*AP*CP*GP*C)-D(P*T)-3') 9 residues - 2499.596 Da.

Residues 1-8 are riboses. Residue 9 is an overhanging deoxythymidine.

1   CGCUPVACGCDT

Entity 2, DNA/RNA (5'-R(GP*CP*GP*UP*AP*CP*GP*C)-D(P*T)-3') 9 residues - 2885.813 Da.

Residues 10-17 are riboses. Residue 18 is an overhanging deoxythymidine.

1   GCGUAGCGDT

Samples:

sample_1: DNA/RNA (5'-R(CP*GP*CP*(UPV)*AP*CP*GP*C)-D(P*T)-3') 0.9 mM; DNA/RNA (5'-R(GP*CP*GP*UP*AP*CP*GP*C)-D(P*T)-3') 0.9 mM

sample_2: DNA/RNA (5'-R(CP*GP*CP*(UPV)*AP*CP*GP*C)-D(P*T)-3') 0.9 mM; DNA/RNA (5'-R(GP*CP*GP*UP*AP*CP*GP*C)-D(P*T)-3') 0.9 mM

sample_conditions_1: ionic strength: 0 M; pH: 6.7; pressure: 1 atm; temperature: 293 K

sample_conditions_2: ionic strength: 0 M; pH: 6.7; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-31P HETCORsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2

Software:

X-PLOR NIH v2.25, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 600 MHz

Related Database Links: