BMRB Entry 34768

Name: Hairpin adopted by modified oligonucleotide A32_mod found in the promoter of AUTS2 gene.
Published: 2023-02-14

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PDB ID: 8bm4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34768
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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:

Hairpin adopted by modified oligonucleotide A32_mod found in the promoter of AUTS2 gene.

Deposition date:

2022-11-10

Original release date:

2023-02-14

Authors:

Novotny, A.

Citation:

Citation: Novotny, A.; Plavec, J.; Kocman, V.. "Structural polymorphism driven by a register shift in a CGAG-rich region found in the promoter of the neurodevelopmental regulator AUTS2 gene" Nucleic Acids Res. 51, 2602-2613 (2023).
PubMed: 36864756

Assembly members:

Assembly members:
entity_1, polymer, 32 residues, 9943.422 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: GAGACGAGCGAGCGAAAGCA CGAACGAGTCTC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	200

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 32 residues - 9943.422 Da.

1

DG

DA

DG

DA

DC

DG

DA

DG

DC

DG

2

DA

DG

DC

DG

DA

DG

DC

DA

3

DC

DG

DA

DC

DG

DA

DG

DT

DC

4

DT

DC

Samples:

sample_1: DNA 0.6 ± 0.06 mM; potassium phosphate 20 ± 2 mM

sample_2: DNA 0.6 ± 0.06 mM; potassium phosphate 20 ± 2 mM

sample_3: DNA, [Residue-specific, 10% 13C/15N], 0.4 ± 0.04 mM; potassium phosphate 20 ± 2 mM

sample_4: DNA, [10 residues, 10% 13C/15N], 0.6 ± 0.06 mM; potassium phosphate 20 ± 2 mM

sample_conditions_1: ionic strength: 20 mM; pH: 7.2; pressure: 1 atm; temperature: 273 K

sample_conditions_2: ionic strength: 20 mM; pH: 7.2; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 20 mM; pH: 7.2; pressure: 1 atm; temperature: 318 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_2	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_3
2D DQF-COSY	sample_1	isotropic	sample_conditions_3
2D 1H-31P CT-COSY	sample_1	isotropic	sample_conditions_3
2D NOESY	sample_1	isotropic	sample_conditions_2
2D DQF-COSY	sample_1	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_3

Software:

TopSpin, Bruker Biospin - collection

NMRFAM-SPARKY, National Magnetic Resonance Facility at Madison - chemical shift assignment, data analysis

Amber v2020, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

NMR spectrometers:

Bruker AVANCE NEO 800 MHz
Bruker AVANCE NEO 600 MHz