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 19861

Title: AFB1 FAPY modified AGT 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*TP*TP*TP*CP*A)-3'), polymer, 10 residues, 3365.322 Da.
DNA_(5'-D(*TP*GP*AP*AP*AP*CP*TP*TP*AP*G)-3'), polymer, 10 residues, 3068.067 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*TP*TP*TP*CP*A)-3'): CTAAXTTTCA
DNA_(5'-D(*TP*GP*AP*AP*AP*CP*TP*TP*AP*G)-3'): TGAAACTTAG

Data sets:
Data typeCount
1H chemical shifts140

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*TP*TP*TP*CP*A)-3')1
2DNA (5'-D(*TP*GP*AP*AP*AP*CP*TP*TP*AP*G)-3')2

Entities:

Entity 1, DNA (5'-D(*CP*TP*AP*AP*(FAG)P*TP*TP*TP*CP*A)-3') 10 residues - 3365.322 Da.

1   DCDTDADAFAGDTDTDTDCDA

Entity 2, DNA (5'-D(*TP*GP*AP*AP*AP*CP*TP*TP*AP*G)-3') 10 residues - 3068.067 Da.

1   DTDGDADADADCDTDTDADG

Samples:

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

sample_condition_AGT_FAPY_modified_duplex_in_D2O: ionic strength: 0.1 M; pH: 7; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H COSYAGT_FAPY_modified_duplexisotropicsample_condition_AGT_FAPY_modified_duplex_in_D2O
2D 1H-1H NOESYAGT_FAPY_modified_duplexisotropicsample_condition_AGT_FAPY_modified_duplex_in_D2O

Software:

SPARKY v3.115, Goddard - chemical shift assignment

TOPSPIN, Bruker Biospin - collection, processing

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

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 900 MHz

Related Database Links: