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 19571

Title: Solution NMR structure of the d(GGGTTTTGGGTGGGTTTTGGG) quadruplex in sodium conditions.   PubMed: 30182059

Authors: Karsisiotis, Andreas Ioannis; Webba da Silva, Mateus; Karsisiotis, Andreas Ioannis

Citation: Dvorkin, Scarlett; Karsisiotis, Andreas; Webba da Silva, Mateus. "Encoding canonical DNA quadruplex structure."  Sci. Adv. 4, eaat3007-eaat3007 (2018).

Assembly members:
DNA, polymer, 21 residues, 6643.305 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: GGGTTTTGGGTGGGTTTTGG G

Data sets:
Data typeCount
1H chemical shifts345

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*G)-3')1

Entities:

Entity 1, DNA (5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*G)-3') 21 residues - 6643.305 Da.

1   DGDGDGDTDTDTDTDGDGDG
2   DTDGDGDGDTDTDTDTDGDG
3   DG

Samples:

Exchangeable_Protons_(278K): DNA (5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*G)-3') 2 mM; sodium phosphate 20 mM; H2O 93%; D2O, [U-100% 2H], 7%

Non_exchangeable_Protons_(293K): DNA (5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*G)-3') 2 mM; sodium phosphate 20 mM; D2O, [U-100% 2H], 100%

Exchangeable_Protons_(278K)_conditions: ionic strength: 20 mM; pH: 7.8; pressure: 1 atm; temperature: 278 K

Non_exchangeable_Protons_(293K)_conditions: ionic strength: 20 mM; pH: 7.8; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYNon_exchangeable_Protons_(293K)isotropicNon_exchangeable_Protons_(293K)_conditions
2D 1H-1H COSYNon_exchangeable_Protons_(293K)isotropicNon_exchangeable_Protons_(293K)_conditions
2D 1H-1H NOESYNon_exchangeable_Protons_(293K)isotropicNon_exchangeable_Protons_(293K)_conditions
2D 1H-1H NOESYExchangeable_Protons_(278K)isotropicExchangeable_Protons_(278K)_conditions
2D 1H-31P HSQCNon_exchangeable_Protons_(293K)isotropicNon_exchangeable_Protons_(293K)_conditions

Software:

FELIX, Accelrys Software Inc. - processing

VNMRJ, Varian - collection

SPARKY, Goddard - chemical shift assignment, data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

  • Varian VNMRS 500 500 MHz

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