BMRB Entry 34679

Title:
10bp DNA/DNA duplex
Deposition date:
2021-11-16
Original release date:
2022-11-08
Authors:
Qiang, L.; Marko, T.; Chaochao, F.; Jialiang, C.; Yifei, Z.; Kuan, L.; Hongjun, L.; Xuncheng, S.; Zhen, X.; Janez, P.; Chuanzheng, Z.
Citation:

Citation: Li, Qiang; Trajkovski, Marko; Fan, Chaochao; Chen, Jialiang; Zhou, Yifei; Lu, Kuan; Li, Hongjun; Su, Xuncheng; Xi, Zhen; Plavec, Janez; Zhou, Chuanzheng. "4'-SCF3 -Labeling Constitutes a Sensitive 19 F NMR Probe for Characterization of Interactions in the Minor Groove of DNA"  Angew. Chem. Int. Ed. Engl. 61, e202201848-e202201848 (2022).
PubMed: 36163470

Assembly members:

Assembly members:
entity_1, polymer, 10 residues, 3003.992 Da.
entity_2, polymer, 10 residues, 3084.041 Da.

Natural source:

Natural source:   Common Name: Octodon degus   Taxonomy ID: 10160   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Octodon degus

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CCATTATAGC
entity_2: GCTATAATGG

Data sets:
Data typeCount
1H chemical shifts188

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 10 residues - 3003.992 Da.

1   DCDCDADTDTDADTDADGDC

Entity 2, unit_2 10 residues - 3084.041 Da.

1   DGDCDTDADTDADADTDGDG

Samples:

sample_1: DNA (5'-D(*CP*CP*AP*TP*TP*AP*TP*AP*GP*C)-3') 0.4 mM; DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3') 0.4 mM; sodium phosphate 10 mM

sample_2: DNA (5'-D(*CP*CP*AP*TP*TP*AP*TP*AP*GP*C)-3') 0.4 mM; DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3') 0.4 mM; sodium phosphate 10 mM

sample_conditions_1: ionic strength: 10 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYsample_1isotropicsample_conditions_1
2D NOESYsample_2isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - chemical shift assignment, collection

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL - chemical shift assignment, peak picking

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

NMR spectrometers:

  • Bruker AVANCE NEO 600 MHz