BMRB Entry 25596

Name: Structure of DNA G-quadruplex adopted by ALS and FTD related GGGGCC repeat with G21 to Br-G21 substitution
Published: 2015-09-21

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PDB ID: 2n2d
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25596
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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:

Structure of DNA G-quadruplex adopted by ALS and FTD related GGGGCC repeat with G21 to Br-G21 substitution

Deposition date:

2015-05-06

Original release date:

2015-09-21

Authors:

Brcic, J.; Plavec, J.

Citation:

Citation: Brcic, J.; Plavec, J.. "Solution structure of a DNA quadruplex containing ALS and FTD related GGGGCC repeat stabilized by 8-bromodeoxyguanosine substitution" Nucleic Acids Res. 43, 8590-8600 (2015).
PubMed: 26253741

Assembly members:

Assembly members:
GGGGCC_repeat_G-quadruplex, polymer, 22 residues, 6957.481 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
GGGGCC_repeat_G-quadruplex: GGGGCCGGGGCCGGGGCCGG XG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	166

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	G-quadruplex	1

Entities:

Entity 1, G-quadruplex 22 residues - 6957.481 Da.

1

DG

DC

DG

2

DC

DG

DC

DG

3

BGM

DG

Samples:

sample_1: dna 0.5 mM; potassium chloride 120 mM; potassium phosphate 20 mM; H2O 90%; D2O 10%

sample_2: dna 0.5 mM; potassium chloride 120 mM; potassium phosphate 20 mM; D2O 100%

sample_3: dna, 8% 13C, 8% 15 N, 0.3 – 0.6 mM; potassium chloride 120 mM; potassium phosphate 20 mM; H2O 90%; D2O 10%

sample_4: dna, 8% 15 N, 0.3 – 0.6 mM; potassium chloride 120 mM; potassium phosphate 20 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 140 mM; pH: 7.2; pressure: 1 atm; temperature: 273 K

sample_conditions_2: ionic strength: 140 mM; pH: 7.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H-1H_TOCSY	sample_2	isotropic	sample_conditions_1
1H-1H_NOESY	sample_1	isotropic	sample_conditions_1
1H_1H_DQF_COSY	sample_2	isotropic	sample_conditions_1
1D_13C__HSQC	sample_3	isotropic	sample_conditions_2
1D_15N_HSQC	sample_4	isotropic	sample_conditions_1
1H-1H_NOESY	sample_2	isotropic	sample_conditions_1

Software:

AMBER v14, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure solution

SPARKY, Goddard - peak picking

NMR spectrometers:

Agilent-Varian Uniform NMR System 600 MHz
Agilent-Varian Uniform NMR System 800 MHz