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 30251

Title: Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd and 9th position and 8-oxoguanine at the 10th position   PubMed: 30289469

Deposition date: 2017-02-24 Original release date: 2017-05-25

Authors: Gruber, D.; Hoppins, J.; Miears, H.; Endutkin, A.; Zharkov, D.; Smirnov, S.

Citation: Gruber, David; Toner, Joanna; Miears, Heather; Shernyukov, Andrey; Kiryutin, Alexey; Lomzov, Alexander; Endutkin, Anton; Grin, Inga; Petrova, Darya; Kupryushkin, Maxim; Yurkovskaya, Alexandra; Johnson, Eric; Okon, Mark; Bagryanskaya, Elena; Zharkov, Dmitry; Smirnov, Serge. "Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation"  Nucleic Acids Res. 46, 10827-10839 (2018).

Assembly members:
entity_1, polymer, 12 residues, 3707.446 Da.

Natural source:   Common Name: not available   Taxonomy ID: 32630   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: CGXGAATTXXCG

Data sets:
Data typeCount
1H chemical shifts176

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21

Entities:

Entity 1, entity_1, 1 12 residues - 3707.446 Da.

1   DCDG5CMDGDADADTDT5CM8OG
2   DCDG

Samples:

sample_1: DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*(DMC)P*(8OG)P*CP*G)-3') 1 mM; EDTA 0.1 mM; potassium chloride 10 mM; sodium chloride 50 mM

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

sample_conditions_2: ionic strength: 120 mM; pH: 6.8; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D DQF-COSYsample_1isotropicsample_conditions_1

Software:

AMBER, CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, DUKE, LUO, ... AND KOLLMAN - refinement

NMRPIPE - structure solution

NMRVIEW - structure solution

NMR spectrometers:

  • Bruker AvanceIII 500 MHz
  • Bruker AvanceIII 600 MHz