BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 18430

Title: Structure and Stability of Duplex DNA Containing (5 S) 5 ,8-Cyclo-2 -Deoxyadenosine: An Oxidative Lesion Repair by NER.   PubMed: 22928555

Authors: Zaliznyak, Tatiana; de los Santos, Carlos; Lukin, Mark

Citation: Zaliznyak, Tatiana; Lukin, Mark; de los Santos, Carlos. "Structure and stability of duplex DNA containing (5'S)-5',8-cyclo-2'-deoxyadenosine: an oxidatively generated lesion repaired by NER."  Chem. Res. Toxicol. 25, 2103-2111 (2012).

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: CGTACXCATGC
11_mer_oligonucleotide_D: GCATGTGTACG

Data sets:
Data typeCount
1H chemical shifts151

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

X represents (5 S) 5 ,8-Cyclo-2 -Deoxyadenosine

1   DCDGDTDADC02IDCDADTDG
2   DC

Entity 2, 11_mer_oligonucleotide_D 11 residues - Formula weight is not available

1   DGDCDADTDGDTDGDTDADC
2   DG

Samples:

sample_1: 11 mer DNA duplex 0.7 mM; 11 mer DNA duplex 0.7 mM; D2O 100%

sample_2: 11 mer DNA duplex 0.7 mM; 11 mer DNA duplex 0.7 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.7; pressure: 1 atm; temperature: 298 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-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1

Software:

VNMR, Varian - collection

TOPSPIN, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

FELIX, Accelrys Software Inc. - processing

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

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

HYPER, Tejero, Monleon, Celda, Powers and Montelione - data analysis, geometry optimization

InsightII, Accelrys Software Inc. - data analysis

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Bruker Avance 400 MHz
  • Bruker Avance 700 MHz

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