BMRB Entry 30198

Name: Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd Position and 9th position
Published: 2017-06-23

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PDB ID: 5trn
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30198
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd Position and 9th position

Deposition date:

2016-10-26

Original release date:

2017-06-23

Authors:

Hoppins, J.; Gruber, D.; Miears, H.; Kasymov, R.; 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:
DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*(DMC)P*GP*CP*G)-3'), 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):
DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*(DMC)P*GP*CP*G)-3'): CGCXAATTXGCG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
1H chemical shifts	170

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, chain 1	1
2	entity_1, chain 2	1

Entities:

Entity 1, entity_1, chain 1 12 residues - 3693.419 Da.

1

DC

DG

DC

8OG

DA

DT

5CM

DG

2

DC

DG

Samples:

sample_1: DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*(DMC)P*GP*CP*G)-3') 1 mM; EDTA 0.1 mM; potassium chloride 10 mM; sodium chloride 50 mM; D2O 100%

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: 274 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D DQF-COSY	sample_1	isotropic	sample_conditions_1

Software:

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

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

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

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

NMR spectrometers:

Bruker AvanceIII 500 MHz
Bruker AvanceIII 500 MHz