BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 15224

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

Data sets:
Data typeCount
1H chemical shifts228

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
11st_strand1
22nd_strand2

Entities:

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

1   DCDCDADADADGORPDADCDC
2   DGDGDG

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

1   DCDCDCDGDGDTDGDCDTDT
2   DTDGDG

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:

NameSampleSample stateSample conditions
2D NOESYsample_1isotropicsample_conditions_1
2D TOCSYsample_1isotropicsample_conditions_1
E-COSYsample_1isotropicsample_conditions_1
H-P HSQCsample_1isotropicsample_conditions_1
H3'-selective HSQCsample_1isotropicsample_conditions_1
watergate-NOESYsample_2isotropicsample_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