BMRB Entry 34942

Name: Solution structure of a silver ion mediated DNA duplex with universal 7-deazapurine substitutions
Published: 2024-09-12

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PDB ID: 9gdm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34942
MolProbity Validation Chart

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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 a silver ion mediated DNA duplex with universal 7-deazapurine substitutions

Deposition date:

2024-08-06

Original release date:

2024-09-12

Authors:

Javornik, U.; Plavec, J.; Galindo, M.

Citation:

Citation: Javornik, U.; Perez-Romero, A.; Lopez-Chamorro, C.; Smith, R.; Dobado, J.; Palacios, O.; Bera, M.; Nyman, M.; Plavec, J.; Galindo, M.. "UNVEILING THE SOLUTION STRUCTURE OF A DNA WITH CONTINUOUS SILVER-MODIFIED WATSON-CRICK BASE PAIRS" Nat. Commun. ., .-..

Assembly members:

Assembly members:
entity_1, polymer, 12 residues, 3657.464 Da.
entity_AG, non-polymer, 107.868 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: XXXCTCXXTCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	89
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
3	unit_3	2
4	unit_4	2
5	unit_5	2
6	unit_6	2
7	unit_7	2
8	unit_8	2
9	unit_9	2
10	unit_10	2
11	unit_11	2
12	unit_12	2
13	unit_13	2
14	unit_14	2

Entities:

Entity 1, unit_1 12 residues - 3657.464 Da.

1

7GU

7DA

DC

DT

DC

7GU

7DA

7GU

DT

2

DC

Entity 2, unit_3 - Ag - 107.868 Da.

1

AG

Samples:

sample_1: DNA 0.8 ± 0.1 mM; NaClO4 100 ± 5 mM; TRIS 100 ± 5 mM; AgNO3 14.5 ± 0.2 mM

sample_2: DNA 0.8 ± 0.1 mM; NaClO4 100 ± 5 mM; TRIS 100 ± 5 mM; AgNO3 14.5 ± 0.2 mM

sample_conditions_1: ionic strength: 100 mM; pH: 8.6; pressure: 1 bar; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-31P HPCOSY	sample_2	isotropic	sample_conditions_1

Software:

VnmrJ v4.2, Agilent - collection

TopSpin v4.1, Bruker - collection, processing

Amber v20, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL (National Magnetic Resonance Facility at Madison) - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE NEO 600 MHz
Varian VNMRS 800 MHz