BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 34436

Title: Guanine-rich oligonucleotide with 5'-GC end form G-quadruplex with A(GGGG)A hexad, GCGC- and G-quartets and two symmetric GG and AA base pairs

Deposition date: 2019-09-25 Original release date: 2020-07-20

Authors: Pavc, D.; Wang, B.; Spindler, L.; Drevensek-Olenik, I.; Plavec, J.; Sket, P.

Citation: Pavc, D.; Wang, B.; Spindler, L.; Drevensek-Olenik, I.; Plavec, J.; Sket, P.. "Guanine-rich oligonucleotide with 5'-GC end form G-quadruplex with A(GGGG)A hexad, GCGC- and G-quartets and two symmetric GG and AA base pairs"  . ., .-..

Assembly members:
entity_1, polymer, 12 residues, 3833.490 Da.

Natural source:   Common Name: not available   Taxonomy ID: 32630   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GCGGAGGGGAGG

Data sets:
Data typeCount
1H chemical shifts115
31P chemical shifts11

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_21

Entities:

Entity 1, unit_1 12 residues - 3833.490 Da.

1   DGDCDGDGDADGDGDGDGDA
2   DGDG

Samples:

sample_1: GCN, [8% 13C; 8% 15N], 1 mM; sodium chloride 100 mM; sodium phosphate buffer 10 mM

sample_2: GCN 1 mM; sodium chloride 175 mM; sodium phosphate buffer 10 mM

sample_3: GCN 1 mM; sodium chloride 175 mM; sodium phosphate buffer 10 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 175 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 175 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYsample_2isotropicsample_conditions_2
2D NOESYsample_2isotropicsample_conditions_2
2D NOESYsample_3isotropicsample_conditions_3
2D NOESYsample_3isotropicsample_conditions_3
2D TOCSYsample_3isotropicsample_conditions_3
2D DQF-COSYsample_2isotropicsample_conditions_2
2D 1H-31P COSYsample_3isotropicsample_conditions_3
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1

Software:

VNMR, Varian - chemical shift assignment, collection, processing

Sparky, Goddard - peak picking

Amber v14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

NMR spectrometers:

  • Agilent Agilent Technologies VNMRS 800 MHz NMR spectrometer 800 MHz
  • Agilent Agilent Technologies DD2 600 MHz NMR spectrometer 600 MHz