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 25369

Title: Solution Structure of DNA Dodecamer with 8-oxoguanine at 10th Position.   PubMed: 27749894

Authors: Gruber, David; Miears, Heather; Hoppins, Joanna; Kiryutin, Aleksey; Kasymov, Rustem; Smirnov, Serge

Citation: Hoppins, Joanna; Gruber, David; Miears, Heather; Kiryutin, Alexey; Kasymov, Rustem; Petrova, Darya; Endutkin, Anton; Popov, Alexander; Yurkovskaya, Alexandra; Fedechkin, Stanislav; Brockerman, Jacob; Zharkov, Dmitry; Smirnov, Serge. "8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme"  PLoS ONE 11, e0164424-e0164424 (2016).

Assembly members:
DNA_(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3'), polymer, 12 residues, 3679.421 Da.

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Data sets:
Data typeCount
1H chemical shifts160

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')_11
2DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')_21


Entity 1, DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')_1 12 residues - 3679.421 Da.

2   DCDG


sample_1: sodium chloride 50 mM; potassium phosphate 10 mM; EDTA 1 mM; DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') 1 mM

sample_2: sodium chloride 50 mM; potassium phosphate 10 mM; EDTA 1 mM; DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') 1 mM

sample_conditions_1: ionic strength: 120 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K


NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1


NMRView v9.0.0-b77, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

X-PLOR_NIH v2.37, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - data analysis, structure solution

NMRPipe v7.9 Rev 2013.021.23.09, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - Structural Modeling, structure solution

NMR spectrometers:

  • Bruker Avance 700 MHz

Related Database Links: