BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 15228

Title: Duplex DNA containing an abasic site with an opposite T (beta anomer) in 5'-G_AC-3' (10 structure ensemble and averaged structure)   PubMed: 18025040

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*TP*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*TP*CP*TP*TP*TP*GP*G)-3': CCCGGTTCTTTGG

Data sets:
Data typeCount
1H chemical shifts225

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   DCDCDADADADGB1PDADCDC
2   DGDGDG

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

1   DCDCDCDGDGDTDTDCDTDT
2   DTDGDG

Samples:

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*TP*CP*TP*TP*TP*GP*G)-3' 2.7 mM; D2O 100%

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*TP*CP*TP*TP*TP*GP*G)-3' 2.7 mM; D2O 10%; H2O 90%

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
H3not available1not available
1not available2not available
1not availablenot availablenot available

Software:

FELIX v2001, Accelrys Inc. - data analysis

MARDIGRAS, James - iterative matrix relaxation

AMBER v8.0, Case et al. - refinement

NMR spectrometers:

  • custom-built custom-built 591 MHz

Related Database Links: