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 18453

Title: NMR structure of duplex DNA containing the -OH-PdG dA base pair: A mutagenic intermediate of acrolein   PubMed: 20049919

Authors: Zaliznyak, Tanya; de los Santos, Carlos; Lukin, Mark; El-khateeb, Mahmoud; Bonala, Rahda; Johnson, Francis

Citation: Zaliznyak, Tanya; de los Santos, Carlos; Lukin, Mark; El-khateeb, Mahmoud; Bonala, Rahda; Johnson, Francis. "NMR structure of duplex DNA containing the -OH-PdG dA base pair: A mutagenic intermediate of acrolein"  Biopolymers 93, 391-401 (2010).

Assembly members:
11_mer_oligonucleotide-B, polymer, 11 residues, Formula weight is not available
11_mer_oligonucleotide-D, polymer, 11 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):
11_mer_oligonucleotide-B: CGTACGCATGC
11_mer_oligonucleotide-D: GCATGAGTACG

Data sets:
Data typeCount
1H chemical shifts150

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
111_mer_oligonucleotide-B1
211_mer_oligonucleotide-D2

Entities:

Entity 1, 11_mer_oligonucleotide-B 11 residues - Formula weight is not available

(aG) : (R)1,N2-a-(OH)-PdG

1   DCDGDTDADCDGDCDADTDG
2   DC

Entity 2, 11_mer_oligonucleotide-D 11 residues - Formula weight is not available

A+: (N1H)+ adenine

1   DGDCDADTDGDADGDTDADC
2   DG

Samples:

sample_1: 11_mer_oligonucleotide-B 0.5 mM; D2O 100%

sample_2: 11_mer_oligonucleotide-B 0.5 mM; D2O 10%; H2O 90%

sample_conditions_1: pH: 6.6; pressure: 1 atm; temperature: 273 K

sample_conditions_2: pH: 6.6; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H COSY45sample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2

Software:

VNMR, Varian - collection

FELIX, Accelrys Software Inc. - chemical shift assignment, data analysis, peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, refinement, structure solution

NMR spectrometers:

  • Varian INOVA 600 MHz

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