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 30329

Title: Solution structure of a DNA dodecamer with 5-methylcytosine at the 3rd and 8-oxoguanine at the 4th position

Authors: Gruber, D.; Shernyukov, A.; Endutkin, A.; Bagryanskaya, E.; Zharkov, D.; Smirnov, S.

Citation: Gruber, D.; Shernyukov, A.; Endutkin, A.; Bagryanskaya, E.; Zharkov, D.; Smirnov, S.. "Solution structure of a DNA dodecamer with 5-methylcytosine at the 3rd and 8-oxoguanine at the 4th position"  . ., .-..

Assembly members:
entity_1, polymer, 12 residues, 3613.439 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: XGXXAATTCGCG

Data sets:
Data typeCount
1H chemical shifts174

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 - 3613.439 Da.

1   DCZDG5CM8OGDADADTDTDCDG
2   DCDG

Samples:

sample_1: DNA (5'-D(*(DC5)P*GP*(DMC)P*(8OG)P*AP*AP*TP*TP*CP*GP*CP*(DG3))-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 atm; temperature: 298 K

sample_conditions_2: ionic strength: 120 mM; pH: 6.8; pressure: 1 atm; temperature: 279 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

Software:

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

CYANA, Guntert, Mumenthaler and Wuthrich - data analysis

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

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

NMR spectrometers:

  • Bruker AvanceIII 600 MHz

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