BMRB Entry 34740

Name: Solution structure of Phen-DC3 intercalating into a quadruplex-duplex hybrid
Published: 2022-10-27

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PDB ID: 8abd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34740
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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:

Solution structure of Phen-DC3 intercalating into a quadruplex-duplex hybrid

Deposition date:

2022-07-04

Original release date:

2022-10-27

Authors:

Vianney, Y.; Weisz, K.

Citation:

Citation: Vianney, Y.; Weisz, K.. "High-affinity binding at quadruplex-duplex junctions: rather the rule than the exception" Nucleic Acids Res. 50, 11948-11964 (2022).
PubMed: 36416262

Assembly members:

Assembly members:
entity_1, polymer, 36 residues, 11210.249 Da.
entity_PQ3, non-polymer, 550.609 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: chemical synthesis

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	41
1H chemical shifts	249

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	2

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

Entity 2, unit_2 - C34 H26 N6 O2 - 550.609 Da.

1

PQ3

Samples:

sample_1: DNA (36-MER) 0.5 mM

sample_conditions_1: ionic strength: 10 mM; pH: 7.0; pressure: 1 atm; temperature: 303 K

Experiments:

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

Software:

Amber v18, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

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

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment, peak picking

TopSpin v4.0.7, Bruker Biospin - data analysis

NMR spectrometers:

Bruker AVANCE NEO 600 MHz