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 15613

Title: SOLUTION STRUCTURE OF THE BIS-C2-2-NAPHTHYLPYRROLO[2,1-c][1,4]BENZODIAZEPINE (DA046) DNA ADDUCT: THE MOLECULAR BASIS FOR DNA HELIX STABILIZATION.   PubMed: 17397227

Deposition date: 2008-01-02 Original release date: 2008-06-26

Authors: Antonow, Dyeison; Barata, Teresa; Jenkins, Terence; Parkinson, Gary; Howard, Philip; Thurston, David; Zloh, Mire

Citation: Antonow, Dyeison; Cooper, Nectaroula; Howard, Philip; Thurston, David. "Parallel Synthesis of a Novel C2-Aryl Pyrrolo[2,1-c][1,4]benzodiazepine (PBD) Library"  J. Comb. Chem. 9, 437-445 (2007).

Assembly members:
DNA_AATCTTTAAAGATT, polymer, 14 residues, 2338.598 Da.
PZD, non-polymer, 386.443 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_AATCTTTAAAGATT: AATCTTTAAAGATT

Data sets:
Data typeCount
1H chemical shifts138

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3')_11
2DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3')_21
3PZD_12
4PZD_22

Entities:

Entity 1, DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3')_1 14 residues - 2338.598 Da.

1   DADADTDCDTDTDTDADADA
2   DGDADTDT

Entity 2, PZD_1 - C24 H22 N2 O3 - 386.443 Da.

1   PZD

Samples:

sample_1: DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3') 0.68 mM; PZD_1 0.68 mM; sodium phosphate 10 mM; sodium chloride 100 mM; D2O, [U-100% 2H], 10%; H2O 90%

sample_conditions_1: ionic strength: 130 mM; pH: 6.85; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

X-PLOR NIH v2.16, Schwieters, Kuszewski, Tjandra and Clore - refinement

TOPSPIN v1.3, Bruker Biospin - collection, processing

AMIX v3.5.5, Bruker Biospin - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker Avance 500 MHz