BMRB Entry 34768

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:
Data typeCount
1H chemical shifts200

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 32 residues - 9943.422 Da.

1   DGDADGDADCDGDADGDCDG
2   DADGDCDGDADADADGDCDA
3   DCDGDADADCDGDADGDTDC
4   DTDC

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:

NameSampleSample stateSample conditions
2D NOESYsample_2isotropicsample_conditions_1
2D NOESYsample_1isotropicsample_conditions_3
2D DQF-COSYsample_1isotropicsample_conditions_3
2D 1H-31P CT-COSYsample_1isotropicsample_conditions_3
2D NOESYsample_1isotropicsample_conditions_2
2D DQF-COSYsample_1isotropicsample_conditions_2
2D 1H-13C HSQCsample_3isotropicsample_conditions_3
2D 1H-13C HSQCsample_4isotropicsample_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