BMRB Entry 18453

Name: NMR structure of duplex DNA containing the -OH-PdG dA base pair: A mutagenic intermediate of acrolein
Published: 2012-06-11

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PDB ID: 2lsz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18453
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of duplex DNA containing the -OH-PdG dA base pair: A mutagenic intermediate of acrolein

Deposition date:

2012-05-09

Original release date:

2012-06-11

Authors:

Zaliznyak, Tanya; de los Santos, Carlos; Lukin, Mark; El-khateeb, Mahmoud; Bonala, Rahda; Johnson, Francis

Citation:

Citation: Zaliznyak, Tanya; de los Santos, Carlos; Lukin, Mark; El-khateeb, Mahmoud; Bonala, Rahda; Johnson, Francis. "NMR structure of duplex DNA containing the -OH-PdG dA base pair: A mutagenic intermediate of acrolein" Biopolymers 93, 391-401 (2010).
PubMed: 20049919

Assembly members:

Assembly members:
11_mer_oligonucleotide-B, polymer, 11 residues, Formula weight is not available
11_mer_oligonucleotide-D, polymer, 11 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 Vector: n/a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
11_mer_oligonucleotide-B: CGTACGCATGC
11_mer_oligonucleotide-D: GCATGAGTACG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	150

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	11_mer_oligonucleotide-B	1
2	11_mer_oligonucleotide-D	2

Entities:

Entity 1, 11_mer_oligonucleotide-B 11 residues - Formula weight is not available

(aG) : (R)1,N2-a-(OH)-PdG

1

DC

DG

DT

DA

DC

DG

DC

DA

DT

DG

2

DC

Entity 2, 11_mer_oligonucleotide-D 11 residues - Formula weight is not available

A+: (N1H)+ adenine

1

DG

DC

DA

DT

DG

DA

DG

DT

DA

DC

2

DG

Samples:

sample_1: 11_mer_oligonucleotide-B 0.5 mM; D2O 100%

sample_2: 11_mer_oligonucleotide-B 0.5 mM; D2O 10%; H2O 90%

sample_conditions_1: pH: 6.6; pressure: 1 atm; temperature: 273 K

sample_conditions_2: pH: 6.6; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY45	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2

Software:

VNMR, Varian - collection

FELIX, Accelrys Software Inc. - chemical shift assignment, data analysis, peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, refinement, structure solution

NMR spectrometers:

Varian INOVA 600 MHz