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 4240

Title: Minor conformer of a benzo[a]pyrene diol epoxide adduct of DA in duplex DNA

Authors: Schwartz, J.; Rice, J.; Luxon, B.; Sayer, J.; Xie, G.; Yeh, H.; Liu, X.; Jerina, D.; Gorenstein, D.

Citation: Schwartz, J.; Rice, J.; Luxon, B.; Sayer, J.; Xie, G.; Yeh, H.; Liu, X.; Jerina, D.; Gorenstein, D.. "Solution structure of the minor conformer of a DNA duplex containing a DG mismatch opposite a benzo[a]pyrene diol epoxide/DA adduct: glycosidic rotation from syn to anti at the modified deoxyadenosine"  Biochemistry 36, 11069-11076 (1997).

Assembly members:
5'-D(GP*GP*TP*CP*AP*CP*GP*AP*G)-3', polymer, 9 residues, Formula weight is not available
(5'-D(CP*TP*CP*GP*GP*GP*AP*CP*C)-3', polymer, 9 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):
5'-D(GP*GP*TP*CP*AP*CP*GP*AP*G)-3': GGTCXCGAG
(5'-D(CP*TP*CP*GP*GP*GP*AP*CP*C)-3': CTCGGGACC

Data sets:
Data typeCount
1H chemical shifts109

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DNA Strand A1
2DNA Strand B2

Entities:

Entity 1, DNA Strand A 9 residues - Formula weight is not available

1   DGDGDTDCABPDCDGDADG

Entity 2, DNA Strand B 9 residues - Formula weight is not available

1   DCDTDCDGDGDGDADCDC

Samples:

sample_1: Duplex DNA (5, -D(GP*GP*TP*CP*AP*CP*GP*AP*G)-3'), ; 1

sample_cond_1: ionic strength: 76 mM; pH: 6.8; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
NOESYsample_1not availablesample_cond_1
ROESYsample_1not availablesample_cond_1
TOCSYsample_1not availablesample_cond_1
2D exchange-only spectrasample_1not availablesample_cond_1

Software:

VNMR v5.1 - Data processing, peak integration, peak picking

MORASS v2.2 - Group developed software used to generate accurate distance restraints from NOE intensities utilizing full relaxation matrix theory.

AMBER v4.1 - Structure calculation using noe restrained molecular dynamics and energy minimization.

NMR spectrometers:

  • Varian UnityPlus 750 MHz
  • Varian UnityPlus 600 MHz

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