BMRB Entry 16138

Name: NMR solution structure of metal-modified DNA
Published: 2012-08-07

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PDB ID: 2m54
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16138
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure of metal-modified DNA

Deposition date:

2009-01-27

Original release date:

2012-08-07

Authors:

Johannsen, Silke; Duepre, Nicole; Boehme, Dominik; Mueller, Jens; Sigel, Roland

Citation:

Citation: Johannsen, Silke; Megger, N.; Boehme, Dominik; Sigel, Roland; Mueller, Jens. "Solution structure of a DNA double helix with consecutive metal-mediated base pairs" Nat. Chem. 2, 229-234 (2010).
PubMed: 21124482

Assembly members:

Assembly members:
DNA_(34-MER), polymer, 34 residues, 8484.617 Da.
AG, non-polymer, 107.868 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available 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):
DNA_(34-MER): TTAATTTXXXAAATTAATTA ATTTXXXAAATTAA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	332

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (34-MER)	1
2	SILVER ION_1	2
3	SILVER ION_2	2
4	SILVER ION_3	2

Entities:

Entity 1, DNA (34-MER) 34 residues - 8484.617 Da.

1

DT

DA

DT

D33

2

DA

DT

DA

DT

DA

3

DA

DT

D33

DA

4

DT

DA

Entity 2, SILVER ION_1 - Ag - 107.868 Da.

1

AG

Samples:

sample_1: DNA (34-MER)0.3 – 0.5 mM; sodium perchlorate 120 mM; SILVER ION0.9 – 1.5 mM

sample_2: DNA (34-MER)0.3 – 0.5 mM; sodium perchlorate 120 mM; SILVER ION0.9 – 1.5 mM

sample_conditions_1: ionic strength: 0.12 M; pD: 7.2; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.12 M; pH: 7.2; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
1D 31P	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2

Software:

TOPSPIN v1.3, 2.0, 2.1, Bruker Biospin - processing

SPARKY v3.1, Goddard - chemical shift assignment, data analysis, peak picking

DYANA v1.5, Guntert, Braun and Wuthrich - structure solution

X-PLOR NIH v2.15, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

Bruker Avance 700 MHz
Bruker AV-2 400 MHz