BMRB Entry 15224
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15224
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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) PubMed: 18025040
Deposition date: 2007-04-25 Original release date: 2008-02-20
Authors: Chen, J.; Dupradeau, F.; Case, D.; Turner, C.; Stubbe, J.
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).
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: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available
Experimental source: Production method: chemical synthesis
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
- assigned_chemical_shifts
Data type | Count |
1H chemical shifts | 228 |
Additional metadata:
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 | DC | DA | DA | DA | DG | ORP | DA | DC | DC | ||||
2 | DG | DG | DG |
Entity 2, 2nd_strand 13 residues - Formula weight is not available
1 | DC | DC | DC | DG | DG | DT | DG | DC | DT | DT | ||||
2 | DT | DG | 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