BMRB Entry 30055

Name: DIY G-Quadruplexes: Solution structure of d(GGTTTGGTTTTGGTTTGG) in sodium
Published: 2017-04-06

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PDB ID: 5j4p
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30055
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: DIY G-Quadruplexes: Solution structure of d(GGTTTGGTTTTGGTTTGG) in sodium PubMed: 30182059

Deposition date: 2016-04-01 Original release date: 2017-04-06

Authors: Dvorkin, S.; Webba da Silva, M.

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

Assembly members:
DNA (5'-D(*GP*GP*TP*TP*TP*GP*GP*TP*TP*TP*TP*GP*GP*TP*TP*TP*GP*G)-3'), polymer, 18 residues, 5630.618 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):
DNA (5'-D(*GP*GP*TP*TP*TP*GP*GP*TP*TP*TP*TP*GP*GP*TP*TP*TP*GP*G)-3'): GGTTTGGTTTTGGTTTGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	193

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 18 residues - 5630.618 Da.

1

DG

DT

DG

DT

2

DT

DG

DT

DG

Samples:

sample_1: DNA, none, 2 ± 0.5 mM; NaPi 100 mM; H2O 90%; D2O 10%

sample_2: DNA, none, 2 ± 0.5 mM; NaPi 100 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 6.8; pressure: 1 atm; temperature: 278.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

Felix, Accelrys Software Inc. - chemical shift assignment

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

Varian VXRS 500 MHz