BMRB Entry 34623

Name: A self-complementary DNA dodecamer duplex contaning 5-hydroxymethylcitosine
Published: 2021-10-30

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PDB ID: 7ogv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34623
MolProbity Validation Chart

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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:

A self-complementary DNA dodecamer duplex contaning 5-hydroxymethylcitosine

Deposition date:

2021-05-07

Original release date:

2021-10-30

Authors:

Battistini, F.; Dans, P.; Terrazas, M.; Castellazzi, C.; Portella, G.; Labrador, M.; Villegas, N.; Brun-Heath, I.; Gonzalez, C.; Orozco, M.

Citation:

Citation: Battistini, F.; Dans, P.; Terrazas, M.; Castellazzi, C.; Portella, G.; Labrador, M.; Villegas, N.; Brun-Heath, I.; Gonzalez, C.; Orozco, M.. "The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function" PLoS Comput. Biol. 17, e1009547-e1009547 (2021).
PubMed: 34748533

Assembly members:

Assembly members:
entity_1, polymer, 12 residues, 3694.406 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CGCGTXGACGCG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	105

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1

Entities:

Entity 1, unit_1 12 residues - 3694.406 Da.

1

DC

DG

DC

DG

DT

5HC

DG

DA

DC

DG

2

DC

DG

Samples:

sample_1: DNA (5'-D(*(DC5)P*GP*CP*GP*TP*(DH)P*GP*AP*CP*GP*CP*(DG3))-3') 1 mM

sample_conditions_1: ionic strength: 125 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K

Experiments:

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

Software:

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

Sparky, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III 600 MHz