BMRB Entry 34914
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34914
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Title: Single acyclic phosphonate nucleotide (S)-ZNA modification on DNA hairpin PubMed: 38687344
Deposition date: 2024-04-25 Original release date: 2024-05-31
Authors: Li, X.; Groaz, E.; Herdewijn, P.; Lescrinier, E.
Citation: Li, X.; Groaz, E.; Herdewijn, P.; Lescrinier, E.. "Impact of Single Acyclic Phosphonate Nucleotide (ZNA) Modifications on DNA Duplex Stability." Chemistry ., e202401254-e202401254 (2024).
Assembly members:
entity_1, polymer, 12 residues, 3635.382 Da.
Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
entity_1: CGCGAATTXGCG
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 78 |
| 1H chemical shifts | 103 |
| 31P chemical shifts | 9 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
Entities:
Entity 1, unit_1 12 residues - 3635.382 Da.
| 1 | DC | DG | DC | DG | DA | DA | DT | DT | L8P | DG | ||||
| 2 | DC | DG |
Samples:
sample_1: Oligo1, [U-1% 13C], 990 ug/mL
sample_2: Oligo1, [U-1% 13C], 990 ug/mL
sample_conditions_1: ionic strength: 0 mM; pH: 6.1; pressure: 1 atm; temperature: 310 K
sample_conditions_2: ionic strength: 0 M; pH: 6.1; pressure: 1 atm; temperature: 310 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HMBC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 2D TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-31P COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D NOESY | sample_2 | isotropic | sample_conditions_2 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
Software:
CARA, Keller and Wuthrich - chemical shift assignment
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation
XEASY, Bartels et al. - peak picking
NMR spectrometers:
- Bruker AVANCE II 600 MHz
- Bruker AVANCE 500 MHz