BMRB Entry 15224

Name: Duplex DNA containing an abasic site with an opposite G (beta anomer) in 5&#039;-G_AC-3&#039; (10 structure ensemble and averaged structure)
Published: 2008-02-20

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15224

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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:

Duplex DNA containing an abasic site with an opposite G (beta anomer) in 5'-G_AC-3' (10 structure ensemble and averaged structure)

Deposition date:

2007-04-25

Original release date:

2008-02-20

Authors:

Chen, J.; Dupradeau, F.; Case, D.; Turner, C.; Stubbe, J.

Citation:

Citation: Chen, J.; Dupradeau, F.; Case, D.; Turner, C.; Stubbe, J.. "DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics." Nucleic Acids Res. 36, 253-262 (2008).
PubMed: 18025040

Assembly members:

Assembly members:
5'-D(*CP*CP*AP*AP*AP*GP*(B1P)P*AP*CP*CP*GP*GP*G)-3', polymer, 13 residues, Formula weight is not available
5'-D(*CP*CP*CP*GP*GP*TP*GP*CP*TP*TP*TP*GP*G)-3', polymer, 13 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(*CP*CP*AP*AP*AP*GP*(B1P)P*AP*CP*CP*GP*GP*G)-3': CCAAAGXACCGGG
5'-D(*CP*CP*CP*GP*GP*TP*GP*CP*TP*TP*TP*GP*G)-3': CCCGGTGCTTTGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	228

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	1st_strand	1
2	2nd_strand	2

Entities:

Entity 1, 1st_strand 13 residues - Formula weight is not available

1

DC

DA

DG

ORP

DA

DC

2

DG

Entity 2, 2nd_strand 13 residues - Formula weight is not available

1

DC

DG

DT

DG

DC

DT

2

DT

DG

Samples:

sample_2: 5'-D(*CP*CP*AP*AP*AP*GP*(B1P)P*AP*CP*CP*GP*GP*G)-3' 2.7 mM; 5'-D(*CP*CP*CP*GP*GP*TP*GP*CP*TP*TP*TP*GP*G)-3' 2.7 mM; D2O 10%; H2O 90%

sample_1: 5'-D(*CP*CP*AP*AP*AP*GP*(B1P)P*AP*CP*CP*GP*GP*G)-3' 2.7 mM; 5'-D(*CP*CP*CP*GP*GP*TP*GP*CP*TP*TP*TP*GP*G)-3' 2.7 mM; D2O 100%

sample_conditions_1: ionic strength: 10 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D TOCSY	sample_1	isotropic	sample_conditions_1
E-COSY	sample_1	isotropic	sample_conditions_1
H-P HSQC	sample_1	isotropic	sample_conditions_1
H3'-selective HSQC	sample_1	isotropic	sample_conditions_1
watergate-NOESY	sample_2	isotropic	sample_conditions_1

Software:

FELIX v2001, Accelrys Inc. - data analysis

MARDIGRAS, Borgias, James - iterative matrix relaxation

NMRView, Johnson, One Moon Scientific - chemical shift assignment

AMBER v8.0, Case et al. - refinement

NMR spectrometers:

custom-built custom-built 591 MHz