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 18638

Title: Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion   PubMed: 22897814

Authors: Zalianyak, Tatiana; de los Santos, Carlos; Lukin, Mark; Attaluri, Sivaprasad; Johnson, Francis

Citation: Lukin, Mark; Zalianyak, Tatiana; Attaluri, Sivaprasad; Johnson, Francis; de los Santos, Carlos. "Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion"  Chem. Res. Toxicol. 25, 2423-2431 (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: GCATGCGTACG

Data sets:
Data typeCount
1H chemical shifts142

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

F : 2,6-diamino-4-hydroxy-5-formamido-2 -deoxypyrimidine

1   DCDGDTDADCLWMDCDADTDG
2   DC

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

1   DGDCDADTDGDCDGDTDADC
2   DG

Samples:

sample_1: 11_mer_oligonucleotide-B 1.1 mM; 11_mer_oligonucleotide-D 1.1 mM; phosphate buffer 25 mM; NaCl 50 mM; EDTA 0.5 mM; D2O 100%

sample_2: 11_mer_oligonucleotide-B 1.1 mM; 11_mer_oligonucleotide-D 1.1 mM; phosphate buffer 25 mM; NaCl 50 mM; EDTA 0.5 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 273 K

sample_conditions_2: pH: 6.8; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2

Software:

TOPSPIN, Bruker Biospin - collection

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

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking, peak volume calc.

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

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links: