BMRB Entry 15360

Name: Solution Structures of a DNA Dodecamer Duplex
Published: 2008-02-29

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15360

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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 Structures of a DNA Dodecamer Duplex PubMed: 17497831

Deposition date: 2007-07-02 Original release date: 2008-02-29

Authors: Bhattacharyya, D.; Wu, Y.; Chaney, S.; Campbell, S.

Citation: Wu, Y.; Bhattacharyya, D.; King, C.; Baskerville-Abraham, I.; Huh, S.; Boysen, G.; Swenberg, J.; Temple, B.; Campbell, S.; Chaney, S.. "Solution structures of a DNA dodecamer duplex with and without a cisplatin 1,2-d(GG) intrastrand cross-link: comparison with the same DNA duplex containing an oxaliplatin 1,2-d(GG) intrastrand cross-link" Biochemistry 46, 6477-6487 (2007).

Assembly members:
CCTCAGGCCTCC, polymer, 12 residues, Formula weight is not available
GGAGGCCTGAGG, polymer, 12 residues, Formula weight is not available

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pBR322

Entity Sequences (FASTA):
CCTCAGGCCTCC: CCTCAGGCCTCC
GGAGGCCTGAGG: GGAGGCCTGAGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	266
31P chemical shifts	22

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA 12mer, chain 1	1
2	DNA 12mer, chain 2	2

Entities:

Entity 1, DNA 12mer, chain 1 12 residues - Formula weight is not available

1

DC

DT

DC

DA

DG

DC

DT

2

DC

Entity 2, DNA 12mer, chain 2 12 residues - Formula weight is not available

1

DG

DA

DG

DC

DT

DG

DA

2

DG

Samples:

sample_1: CCTCAGGCCTCC 1.0 mM; GGAGGCCTGAGG 1.0 mM; NaCl 100 mM; phosphate buffer 5 mM

sample_2: CCTCAGGCCTCC 1.0 mM; GGAGGCCTGAGG 1.0 mM; NaCl 100 mM; phosphate buffer 5 mM

sample_conditions_1: ionic strength: 105 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

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

Software:

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMRPipe v1.1, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 800 MHz