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 19863

Title: AFB1 FAPY modified AG(7-deaza)G duplex   PubMed: 25587868

Authors: Li, Liang; Stone, Michael

Citation: Li, Liang; Brown, Kyle; Ma, Ruidan; Stone, Michael. "DNA Sequence Modulates Geometrical Isomerism of the trans-8,9-Dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy Aflatoxin B1 Adduct"  Chem. Res. Toxicol. 28, 225-237 (2015).

Assembly members:
DNA_(5'-D(*CP*TP*AP*AP*(FAG)P*(7GU)P*TP*TP*CP*A)-3'), polymer, 10 residues, 3042.111 Da.
DNA_(5'-D(*TP*GP*AP*AP*CP*CP*TP*TP*AP*G)-3'), polymer, 10 residues, 3044.042 Da.

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_(5'-D(*CP*TP*AP*AP*(FAG)P*(7GU)P*TP*TP*CP*A)-3'): CTAAXXTTCA
DNA_(5'-D(*TP*GP*AP*AP*CP*CP*TP*TP*AP*G)-3'): TGAACCTTAG

Data sets:
Data typeCount
1H chemical shifts128

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*CP*TP*AP*AP*(FAG)P*(7GU)P*TP*TP*CP*A)-3')1
2DNA (5'-D(*TP*GP*AP*AP*CP*CP*TP*TP*AP*G)-3')2

Entities:

Entity 1, DNA (5'-D(*CP*TP*AP*AP*(FAG)P*(7GU)P*TP*TP*CP*A)-3') 10 residues - 3042.111 Da.

1   DCDTDADAFAG7GUDTDTDCDA

Entity 2, DNA (5'-D(*TP*GP*AP*AP*CP*CP*TP*TP*AP*G)-3') 10 residues - 3044.042 Da.

1   DTDGDADADCDCDTDTDADG

Samples:

AG(7-deaza)G: DNA (5'-D(*CP*TP*AP*AP*(FAG)P*(7GU)P*TP*TP*CP*A)-3') 0.5 mM; DNA (5'-D(*TP*GP*AP*AP*CP*CP*TP*TP*AP*G)-3') 0.5 mM; Sodium Chloride 100 mM; Sodium Phosphate 10 mM; EDTA 50 uM

sample_condition_AG(7-deaza)G: ionic strength: 0.1 M; pH: 7; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H COSYAG(7-deaza)Gisotropicsample_condition_AG(7-deaza)G
2D 1H-1H NOESYAG(7-deaza)Gisotropicsample_condition_AG(7-deaza)G

Software:

AMBER v12, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

TOPSPIN v3, Bruker Biospin - collection, processing

SPARKY v3.115, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 900 MHz

Related Database Links: