BMRB Entry 4240

Name: Minor conformer of a benzo[a]pyrene diol epoxide adduct of DA in duplex DNA
Published: 2000-05-01

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR4240

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

1998-10-08

Original release date:

2000-05-01

Authors:

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

Citation:

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:

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:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

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:

assigned_chemical_shifts
- chem_shift_set_1
- chem_shift_set_2

Data type	Count
1H chemical shifts	109

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA Strand A	1
2	DNA Strand B	2

Entities:

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

1

DG

DT

DC

ABP

DC

DG

DA

DG

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

1

DC

DT

DC

DG

DA

DC

Samples:

sample_1: Duplex DNA (5'-D(GP*GP*TP*CP*AP*CP*GP*AP*G)-3') (DOT)(5'-D(CP*TP*CP*GP*GP*GP*AP*CP*C)-3') 180 A260 units

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

Experiments:

Name	Sample	Sample state	Sample conditions
NOESY	sample_1	not available	sample_cond_1
ROESY	sample_1	not available	sample_cond_1
TOCSY	sample_1	not available	sample_cond_1
2D exchange-only spectra	sample_1	not available	sample_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