BMRB Entry 34228

Name: DNA-RNA Hybrid Quadruplex with Flipped Tetrad
Published: 2018-09-19

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PDB ID: 6ffr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34228
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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:

DNA-RNA Hybrid Quadruplex with Flipped Tetrad

Deposition date:

2018-01-09

Original release date:

2018-09-19

Authors:

Haase, L.; Dickerhoff, J.; Weisz, K.

Citation:

Citation: Haase, L.; Dickerhoff, J.; Weisz, K.. "DNA-RNA Hybrid Quadruplexes Reveal Interactions that Favor RNA Parallel Topologies" Chemistry 24, 15365-15371 (2018).
PubMed: 30084512

Assembly members:

Assembly members:
entity_1, polymer, 22 residues, 7004.491 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: GGGATGGGACACAGGGGACG GG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	21
1H chemical shifts	142

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 22 residues - 7004.491 Da.

1

G

DG

DA

DT

DG

DA

DC

2

DA

DC

DA

DG

DA

DC

G

3

DG

Samples:

sample_1: potassium phosphate 10 mM; entity_1 0.48 mM

sample_2: potassium phosphate 10 mM; entity_1 0.48 mM

sample_conditions_1: ionic strength: 10 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY mixing time 500 ms	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY mixing time 300 ms	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY mixing time 150 ms	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY mixing time 80 ms	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY mixing time 300 ms	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1

Software:

TOPSPIN v3.5, Bruker Biospin - processing

Analysis v2.4, CCPN - chemical shift assignment, peak picking

X-PLOR NIH v2.46, Schwieters, Kuszewski, Tjandra and Clore - refinement

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

NMR spectrometers:

Bruker Avance 600 MHz