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 25672

Title: Base-displaced intercalated structure of the N-(2'deoxyguanosin-8-yl)-3-aminobenzanthrone DNA adduct   PubMed: 26641105

Authors: Politica, Dustin; Stone, Michael; Malik, Chanchal; Basu, Ashis

Citation: Politica, Dustin; Malik, Chanchal; Basu, Ashis; Stone, Michael. "Base-Displaced Intercalated Structure of the N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone DNA Adduct"  Chem. Res. Toxicol. 28, 2253-2266 (2015).

Assembly members:
DNA_(5'-D(*GP*TP*GP*CP*(ABG)P*TP*GP*TP*TP*TP*GP*T)-3'), polymer, 12 residues, 3873.430 Da.
DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'), polymer, 12 residues, 3609.425 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
DNA_(5'-D(*GP*TP*GP*CP*(ABG)P*TP*GP*TP*TP*TP*GP*T)-3'): GTGCXTGTTTGT
DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'): ACAAACACGCAC

Data sets:
Data typeCount
1H chemical shifts184

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*GP*TP*GP*CP*(ABG)P*TP*GP*TP*TP*TP*GP*T)-3')1
2DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3')2

Entities:

Entity 1, DNA (5'-D(*GP*TP*GP*CP*(ABG)P*TP*GP*TP*TP*TP*GP*T)-3') 12 residues - 3873.430 Da.

1   DGDTDGDC4E9DTDGDTDTDT
2   DGDT

Entity 2, DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') 12 residues - 3609.425 Da.

1   DADCDADADADCDADCDGDC
2   DADC

Samples:

sample_1: DNA (5'-D(*GP*TP*GP*CP*(ABG)P*TP*GP*TP*TP*TP*GP*T)-3') 352 uM; DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') 352 uM; sodium phosphate 10 mM; sodium chloride 100 mM; EDTA 50 uM

sample_2: DNA (5'-D(*GP*TP*GP*CP*(ABG)P*TP*GP*TP*TP*TP*GP*T)-3') 521 uM; DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') 521 uM; sodium phosphate 10 mM; sodium chloride 100 mM; EDTA 50 uM

sample_conditions_1: ionic strength: 110 mM; pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 110 mM; pH: 7; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-1H COSYsample_2isotropicsample_conditions_2

Software:

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

SPARKY, Goddard - chemical shift assignment, data analysis

TOPSPIN, Bruker Biospin - data analysis, processing

MARDIGRAS, Borgias, B. A. & James, T. L. - Restraint calculation

CORMA, Borgias, B. A. & James, T. L. - Validation

NMR spectrometers:

  • Bruker Avance 900 MHz

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