BMRB Entry 18638

Name: Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion
Published: 2013-02-18

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PDB ID: 2lwm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18638
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion

Deposition date:

2012-08-03

Original release date:

2013-02-18

Authors:

Zalianyak, Tatiana; de los Santos, Carlos; Lukin, Mark; Attaluri, Sivaprasad; Johnson, Francis

Citation:

Citation: Lukin, Mark; Zalianyak, Tatiana; Attaluri, Sivaprasad; Johnson, Francis; de los Santos, Carlos. "Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion" Chem. Res. Toxicol. 25, 2423-2431 (2012).
PubMed: 22897814

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
11_mer_oligonucleotide-B: CGTACXCATGC
11_mer_oligonucleotide-D: GCATGCGTACG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	142

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

F : 2,6-diamino-4-hydroxy-5-formamido-2 -deoxypyrimidine

1

DC

DG

DT

DA

DC

LWM

DC

DA

DT

DG

2

DC

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

1

DG

DC

DA

DT

DG

DC

DG

DT

DA

DC

2

DG

Samples:

sample_1: 11_mer_oligonucleotide-B 1.1 mM; 11_mer_oligonucleotide-D 1.1 mM; phosphate buffer 25 mM; NaCl 50 mM; EDTA 0.5 mM; D2O 100%

sample_2: 11_mer_oligonucleotide-B 1.1 mM; 11_mer_oligonucleotide-D 1.1 mM; phosphate buffer 25 mM; NaCl 50 mM; EDTA 0.5 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 273 K

sample_conditions_2: pH: 6.8; pressure: 1 atm; 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 DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2

Software:

TOPSPIN, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking, peak volume calc.

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

NMR spectrometers:

Bruker Avance 800 MHz