BMRB Entry 30151

Title:
Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th Position
Deposition date:
2016-08-01
Original release date:
2016-12-16
Authors:
Miears, H.; Hoppins, J.; Gruber, D.; Kasymov, R.; Johnson, E.; 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, 3677.419 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: CGCGAATTXGCG

Data sets:
Data typeCount
1H chemical shifts190

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 - 3677.419 Da.

1   DCDGDCDGDADADTDT5CMDG
2   DCDG

Samples:

sample_1: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(DMC)P*GP*CP*G)-3') 1 mM; EDTA 0.1 mM; potassium phosphate 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 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1

Software:

AMBER v12, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement, structure calculation

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

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

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

NMRView v9.0, Johnson, One Moon Scientific - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker Avance 500 MHz