BMRB Entry 36326

Name: NMR solution structure of a DNA minidumbbell containing an abasic bulge between two CCTG repeats
Published: 2021-05-11

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PDB ID: 6m6k
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36326
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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:

NMR solution structure of a DNA minidumbbell containing an abasic bulge between two CCTG repeats

Deposition date:

2020-03-15

Original release date:

2021-05-11

Authors:

Wan, L.; Lam, S.; Guo, P.

Citation:

Citation: Wan, L.; Lam, S.; Lee, H.; Guo, P.. "Rational Design of a Reversible Mg2+/EDTA-controlled Molecular Switch Based on a DNA Minidumbbell" Chem.Commun.(Camb.) 56, 10127-10130 (2020).
PubMed: 32870195

Assembly members:

Assembly members:
entity_1, polymer, 9 residues, 2558.663 Da.
SODIUM ION, non-polymer, 22.990 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CCTGXCCTG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	92

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2
3	entity_2	2
4	entity_2	2
5	entity_2	2
6	entity_2	2
7	entity_2	2
8	entity_2	2
9	entity_2	2

Entities:

Entity 1, entity_1 9 residues - 2558.663 Da.

1

DC

DT

DG

3DR

DC

DT

DG

Entity 2, entity_2 - Na - 22.990 Da.

1

NA

Samples:

sample_1: DNA 0.2 ± 0.1 mM; DSS 0.02 ± 0.001 mM; NaPi 10 ± 0.1 mM; D2O, [U-2H], 99.96%

sample_conditions_1: ionic strength: 10 mM; pH: 7.0; pressure: 1 atm; temperature: 273 K

Experiments:

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

Software:

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

TopSpin, Bruker - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III 700 MHz
Bruker AVANCE 500 MHz