BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 19222

Title: NMR Studies of DNA Support the Role of Pre-Existing Minor Groove Variations in Nucleosome Indirect Readout   PubMed: 25102280

Authors: Xu, Xiaoqian; Ben Imeddourene, Akli; Zargarian, Loussine; Foloppe, Nicolas; Mauffret, Olivier; Hartmann, Brigitte

Citation: Xu, Xiaoqian; Ben Imeddourene, Akli; Zargarian, Loussine; Foloppe, Nicolas; Mauffret, Olivier; Hartmann, Brigitte. "NMR Studies of DNA Support the Role of Pre-Existing Minor Groove Variations in Nucleosome Indirect Readout"  Biochemistry 53, 5601-5612 (2014).

Assembly members:
DNA_dodecamer_1-1, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_1-2, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_2-1, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_2-2, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_3-1, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_3-2, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_4-1, polymer, 12 residues, Formula weight is not available
DNA_dodecamer_4-2, polymer, 12 residues, Formula weight is not available

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

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
DNA_dodecamer_1-1: TCGTAGCAAGCT
DNA_dodecamer_1-2: AGCTTGCTACGA
DNA_dodecamer_2-1: GCTCTAGCACCG
DNA_dodecamer_2-2: CGGTGCTAGAGC
DNA_dodecamer_3-1: CCGCTTAAACGC
DNA_dodecamer_3-2: GCGTTTAAGCGG
DNA_dodecamer_4-1: CGCACGTACGCG
DNA_dodecamer_4-2: CGCGTACGTGCG

Data typeCount
31P chemical shifts264

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA dodecamer 1-11
2DNA dodecamer 1-22
3DNA dodecamer 2-13
4DNA dodecamer 2-24
5DNA dodecamer 3-15
6DNA dodecamer 3-26
7DNA dodecamer 4-17
8DNA dodecamer 4-28

Entities:

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

1   DTDCDGDTDADGDCDADADG
2   DCDT

Entity 2, DNA dodecamer 1-2 12 residues - Formula weight is not available

1   DADGDCDTDTDGDCDTDADC
2   DGDA

Entity 3, DNA dodecamer 2-1 12 residues - Formula weight is not available

1   DGDCDTDCDTDADGDCDADC
2   DCDG

Entity 4, DNA dodecamer 2-2 12 residues - Formula weight is not available

1   DCDGDGDTDGDCDTDADGDA
2   DGDC

Entity 5, DNA dodecamer 3-1 12 residues - Formula weight is not available

1   DCDCDGDCDTDTDADADADC
2   DGDC

Entity 6, DNA dodecamer 3-2 12 residues - Formula weight is not available

1   DGDCDGDTDTDTDADADGDC
2   DGDG

Entity 7, DNA dodecamer 4-1 12 residues - Formula weight is not available

1   DCDGDCDADCDGDTDADCDG
2   DCDG

Entity 8, DNA dodecamer 4-2 12 residues - Formula weight is not available

1   DCDGDCDGDTDADCDGDTDG
2   DCDG

Samples:

sample_1: DNA dodecamer 1-1 1.5 ± 0.05 mM; DNA dodecamer 1-2 1.5 ± 0.05 mM; DNA dodecamer 2-1 1.5 ± 0.05 mM; DNA dodecamer 2-2 1.5 ± 0.05 mM; DNA dodecamer 3-1 1.5 ± 0.05 mM; DNA dodecamer 3-2 1.5 ± 0.05 mM; DNA dodecamer 4-1 1.5 ± 0.05 mM; DNA dodecamer 4-2 1.5 ± 0.05 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 293 K

sample_conditions_2: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 303 K

sample_conditions_3: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 313 K

sample_conditions_4: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_4
2D 1H-13C TROSYsample_1anisotropicsample_conditions_4
2D 1H-13C HSQCsample_1anisotropicsample_conditions_4
2D 1H-31P Hetero - Correlationsample_1isotropicsample_conditions_1

Software:

SPARKY, T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco - chemical shift assignment

NMRPIPE v8.2, F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Bax: NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR. 6, 277-293 (1995). - processing

NMR spectrometers:

  • Bruker Avance 500 MHz

Related Database Links: