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 17697

Title: Structure of a dimeric all-parallel-stranded G-quadruplex stacked via the 5'-to-5' interface   PubMed: 21840903

Authors: Do, Ngoc Quang; Lim, Kah Wai; Teo, Ming Hoon; Heddi, Brahim; Phan, Anh Tuan

Citation: Do, Ngoc Quang; Lim, Kah Wai; Teo, Ming Hoon; Heddi, Brahim; Phan, Anh Tuan. "Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity."  Nucleic Acids Res. 39, 9448-9457 (2011).

Assembly members:
DNA_(5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')_, polymer, 16 residues, 5107.312 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):
DNA_(5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')_: GXGTGGGTGGGTGGGT

Data sets:
Data typeCount
1H chemical shifts127

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1G-quadruplex_strand_11
2G-quadruplex_strand_21

Entities:

Entity 1, G-quadruplex_strand_1 16 residues - 5107.312 Da.

1   DGDIDGDTDGDGDGDTDGDG
2   DGDTDGDGDGDT

Samples:

sample_1: G-quadruplex0.5 – 2.0 mM; H2O 90%; D2O 10%

sample_2: G-quadruplex0.5 – 2.0 mM; D2O 100%

sample_3: G-quadruplex, [U-2% 15N; U-2% 13C], 0.5 – 2.0 mM; H2O 90%; D2O 10%

sample_4: G-quadruplex, [U-100% 2H], 0.5 – 2.0 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 90 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C JR HMBCsample_1isotropicsample_conditions_1
2D 1H-1H JR NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H COSYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
H-D exchangesample_2isotropicsample_conditions_1
15N-filteredsample_3isotropicsample_conditions_1
D-labeledsample_4isotropicsample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - processing

FELIX v2007, Felix NMR, Inc. - peak picking

X-PLOR NIH v2.27, Schwieters, Kuszewski, Tjandra and Clore - structure solution

AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 700 MHz

Related Database Links: