BMRB Entry 34805

Title:
Solution structure of the 8-17 DNAzyme in presence of Zn2+
Deposition date:
2023-04-13
Original release date:
2023-04-19
Authors:
Andralojc, W.; Gdaniec, Z.
Citation:

Citation: Wieruszewska, Julia; Pawlowicz, Aleksandra; Polomska, Ewa; Pasternak, Karol; Gdaniec, Zofia; Andralojc, Witold. "The 8-17 DNAzyme can operate in a single active structure regardless of metal ion cofactor"  Nat. Commun. 15, 4218-4218 (2024).
PubMed: 38760331

Assembly members:

Assembly members:
entity_1, polymer, 35 residues, 10841.923 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: CGCCGGGGTCGAAGACTGCC AGCGGCTCGACGGCG

Data sets:
Data typeCount
1H chemical shifts302
31P chemical shifts32

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 35 residues - 10841.923 Da.

1   DCDGDCDCDGDGDGDGDTDC
2   DGDADADGDADCDTDGDCDC
3   DADGDCDGDGDCDTDCDGDA
4   DCDGDGDCDG

Samples:

sample_1: 8-17 DNAzyme 2.2 mM; cacodylate 10 mM; zinc chloride 4 mM; sodium chloride 200 mM

sample_2: 8-17 DNAzyme 2.2 mM; cacodylate 10 mM; zinc chloride 4 mM; sodium chloride 200 mM

sample_conditions_1: ionic strength: 200 mM; pH: 6.0; pressure: 1 atm; temperature: 308 K

sample_conditions_2: ionic strength: 200 mM; pH: 6.0; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-31P COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2

Software:

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

NMRFAM-SPARKY, NMRFAM - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker AVANCE III 700 MHz