BMRB Entry 19279

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19279
MolProbity Validation Chart

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Title:
Structure of d[GGGAAGGGCGCGAAGCATTCGCGAGGTAGG] duplex-quadruplex hybrid
Deposition date:
2013-05-30
Original release date:
2013-07-08
Authors:
Lim, Kah Wai; Phan, Anh Tuan
Citation:

Citation: Lim, Kah Wai; Phan, Anh Tuan. "Structural basis of DNA quadruplex-duplex junction formation."  Angew. Chem. Int. Ed. Engl. 52, 8566-8569 (2013).
PubMed: 23794476

Assembly members:

Assembly members:
DNA_(30-MER), polymer, 30 residues, 9444.141 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_(30-MER): GGGAAGGGCGCGAAGCATTC GCGAGGTAGG

Data sets:
Data typeCount
1H chemical shifts245

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (30-MER)1

Entities:

Entity 1, DNA (30-MER) 30 residues - 9444.141 Da.

1   DGDGDGDADADGDGDGDCDG
2   DCDGDADADGDCDADTDTDC
3   DGDCDGDADGDGDTDADGDG

Samples:

DNA-1: DNA (30-MER) 0.5-2.0 mM; H2O 90%; D2O 10%

DNA-2: DNA (30-MER) 0.5-2.0 mM

DNA-3: DNA (30-MER), [U-2% 15N], 0.5-2.0 mM

DNA-4: DNA (30-MER), [U-100% 2H], 0.5-2.0 mM

sample_conditions_1: ionic strength: 40 mM; pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 40 mM; pH: 7; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYDNA-2isotropicsample_conditions_1
2D 1H-1H JR NOESYDNA-1isotropicsample_conditions_1
2D 1H-1H JR NOESYDNA-1isotropicsample_conditions_2
2D 1H-1H COSYDNA-2isotropicsample_conditions_1
2D 1H-1H TOCSYDNA-2isotropicsample_conditions_1
2D 1H-13C HSQCDNA-2isotropicsample_conditions_1
2D 1H-13C JR HMBCDNA-1isotropicsample_conditions_1
2D 1H-31P HSQCDNA-2isotropicsample_conditions_1
H-D EXCHANGEDNA-2isotropicsample_conditions_1
15N-FILTEREDDNA-3isotropicsample_conditions_1
15N-FILTEREDDNA-3isotropicsample_conditions_2
D-LABELEDDNA-4isotropicsample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - processing

FELIX v2007, Felix NMR, Inc. - peak picking

X-PLOR NIH v2.29, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

  • Bruker Avance 400 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 700 MHz