BMRB Entry 30250

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

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).
PubMed: 30289469

Assembly members:

Assembly members:
entity_1, polymer, 12 residues, 3693.419 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CGXGAATTCXCG

Data sets:
Data typeCount
1H chemical shifts170

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 - 3693.419 Da.

1   DCDG5CMDGDADADTDTDC8OG
2   DCDG

Samples:

sample_1: DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*(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 .; temperature: 298 K

sample_conditions_2: ionic strength: 120 mM; pH: 6.8; pressure: 1 .; 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, structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker AvanceIII 500 MHz
  • Bruker AvanceIII 600 MHz