BMRB Entry 34664

Name: Parallel Q-D hybrid with 3&#039; duplex stem-loop as a lateral snapback loop
Published: 2021-12-17

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PDB ID: 7pne
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34664
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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:

Parallel Q-D hybrid with 3' duplex stem-loop as a lateral snapback loop

Deposition date:

2021-09-06

Original release date:

2021-12-17

Authors:

Vianney, Y.; Weisz, K.

Citation:

Citation: Vianney, Y.; Weisz, K.. "Indoloquinoline Ligands Favor Intercalation at Quadruplex-Duplex Interfaces" Chemistry 28, e202103718-e202103718 (2022).
PubMed: 34905232

Assembly members:

Assembly members:
entity_1, polymer, 36 residues, 11210.249 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: synthetic construct

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XTAGGTGGGTAGGGTGGGCT AGTCATTTTGACTAGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	42
1H chemical shifts	250

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 36 residues - 11210.249 Da.

1

THM

DT

DA

DG

DT

DG

DT

2

DA

DG

DT

DG

DC

DT

3

DA

DG

DT

DC

DA

DT

DG

4

DA

DC

DT

DA

DG

Samples:

sample_1: DNA 1 mM; potassium phosphate buffer 10 mM

sample_conditions_1: ionic strength: 10 mM; pH: 7.0; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1

Software:

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment, data analysis

TopSpin v4.0.7, Bruker Biospin - processing

X-PLOR NIH v3.0.3, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

Amber v16, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Bruker AVANCE NEO 600 MHz