BMRB Entry 19035

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19035
MolProbity Validation Chart

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Title:
G-rich VEGF aptamer with LNA modifications
Deposition date:
2013-02-13
Original release date:
2013-08-14
Authors:
Marusic, Maja; Veedu, Rakesh; Plavec, Janez
Citation:

Citation: Marusic, Maja; Veedu, Rakesh; Wengel, Jesper; Plavec, Janez. "G-rich VEGF aptamer with locked and unlocked nucleic acid modifications exhibits a unique G-quadruplex fold."  Nucleic Acids Res. 41, 9524-9536 (2013).
PubMed: 23935071

Assembly members:

Assembly members:
DNA-RNA_(25-MER), polymer, 25 residues, 8001.162 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA-RNA_(25-MER): TGTGXGGGTGGACGGGCCGG XTAXA

Data sets:
Data typeCount
1H chemical shifts189

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA/RNA (25-MER)1

Entities:

Entity 1, DNA/RNA (25-MER) 25 residues - 8001.162 Da.

1   DTDGDTDGLCGDGDGDGDTDG
2   DGDADCDGDGDGDCDCDGDG
3   LCGDTDALCGDA

Samples:

sample_1: DNA/RNA (25-MER) 0.5 mM; potassium phosphate 10 mM; potassium chloride 90 mM; H2O 90%; D2O 10%

sample_2: DNA/RNA (25-MER) 0.5 mM; potassium phosphate 10 mM; potassium chloride 40 mM; H2O 90%; D2O 10%

sample_3: DNA/RNA (25-MER) 0.5 mM; potassium phosphate 10 mM; potassium chloride 90 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 273 K

sample_conditions_2: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_3isotropicsample_conditions_2
2D DQF-COSYsample_3isotropicsample_conditions_2
2D 1H-1H COSYsample_3isotropicsample_conditions_2
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_2isotropicsample_conditions_3
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

AMBER v11, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - data analysis, refinement, structure solution

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment, peak picking

VNMRJ, Agilent Technologies - collection

NMR spectrometers:

  • Varian/Agilent VNMRS 600 MHz
  • Varian/Agilent VNMRS 800 MHz