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 5730

Title: 1H Chemical Shift Assignments for a DNA Duplex with N6-Deoxyadenosine Adduct of (9S,10R)-9,10-Epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene   PubMed: 12578353

Authors: Volk, D.; Thiviyanathan, V.; Rice, J.; Luxon, B.; Shah, J.; Yagi, H.; Sayer, J.; Yeh, H.; Jerina, D.; Gorenstein, D.

Citation: Volk, David; Thiviyanathan, Varatharasa; Rice, Jeffrey; Luxon, Bruce; Shah, Jamshed; Yagi, Haruhiko; Sayer, Jane; Yeh, Herman; Jerina, Donald; Gorenstein, David. "Solution Structure of a Cis-Opened (10R)-N6-Deoxyadenosine Adduct of (9S,10R)-(9,10)-Epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a DNA Duplex"  Biochemistry 42, 1410-1420 (2003).

Assembly members:
Benzo[a]pyrene adducted DNA duplex, polymer, 11 residues, Formula weight is not available
Benzo[a]pyrene adducted DNA duplex, polymer, 11 residues, Formula weight is not available
1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE, non-polymer, 304.339 Da.

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: Eukaryota   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
Benzo[a]pyrene adducted DNA duplex: CGGTCACGAGG
Benzo[a]pyrene adducted DNA duplex: CCTCGTGACCG

Data typeCount
1H chemical shifts234

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1Strand11
2Strand22
37,8,9,10-tetrahydro benzo[a]pyrene3

Entities:

Entity 1, Strand1 11 residues - Formula weight is not available

1   DCDGDGDTDCDADCDGDADG
2   DG

Entity 2, Strand2 11 residues - Formula weight is not available

1   DCDCDTDCDGDTDGDADCDC
2   DG

Entity 3, 7,8,9,10-tetrahydro benzo[a]pyrene - C20 H16 O3 - 304.339 Da.

1   BAP

Samples:

sample_1: Benzo[a]pyrene adducted DNA duplex 1.5 mM; Benzo[a]pyrene adducted DNA duplex 1.5 mM; (-)-7S,8R,9R-TRIHYDROXY-7,8,9,10-TETRAHYDRO BENZO[A]PYRENE 1.5 mM; Phosphates 20 mM; NaCl 57 mM; sodium azide 0.5 mM; H2O 90%; D2O 10%

sample_2: Benzo[a]pyrene adducted DNA duplex 1.5 mM; Benzo[a]pyrene adducted DNA duplex 1.5 mM; (-)-7S,8R,9R-TRIHYDROXY-7,8,9,10-TETRAHYDRO BENZO[A]PYRENE 1.5 mM; Phosphates 20 mM; NaCl 57 mM; sodium azide 0.5 mM; D2O 99.96%

sample_cond_1: ionic strength: 100 mM; pH: 6.7; pressure: 1 atm; temperature: 278 K

sample_cond_2: ionic strength: 100 mM; pH*: 6.7; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYnot availablenot availablenot available
2D TOCSYnot availablenot availablenot available
2D ROESYnot availablenot availablenot available
Exchange-Onlynot availablenot availablenot available

Software:

VNMR v6.1 - collection, data analysis

MORASS v2.51 - iterative matrix relaxation

AMBER v5.0, 6.0, and 7.0 - refinement

NMR spectrometers:

  • Varian UNITYplus 600 MHz
  • Varian Unityplus 750 MHz

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