BMRB Entry 34436

Name: 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
Published: 2020-07-20

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PDB ID: 6sx6
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34436
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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:

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:

Citation: Pavc, D.; Wang, B.; Spindler, L.; Drevensek-Olenik, I.; Plavec, J.; Sket, P.. "GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly" Nucleic Acids Res. 48, 2749-2761 (2020).
PubMed: 31996902

Assembly members:

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

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GCGGAGGGGAGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	115
31P chemical shifts	11

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1

Entities:

Entity 1, unit_1 12 residues - 3833.490 Da.

1

DG

DC

DG

DA

DG

DA

2

DG

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:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_2	isotropic	sample_conditions_2
2D NOESY	sample_2	isotropic	sample_conditions_2
2D NOESY	sample_3	isotropic	sample_conditions_3
2D NOESY	sample_3	isotropic	sample_conditions_3
2D TOCSY	sample_3	isotropic	sample_conditions_3
2D DQF-COSY	sample_2	isotropic	sample_conditions_2
2D 1H-31P COSY	sample_3	isotropic	sample_conditions_3
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_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