BMRB Entry 36455

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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/BMR36455
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
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Title:
C4'-SCF3-DT modifeid DNA-DNA duplex
Deposition date:
2021-11-18
Original release date:
2025-11-01
Authors:
Li, Q.; Trajkovski, M.; Fan, C.; Chen, J.; Zhou, Y.; Lu, K.; Li, H.; Su, X.; Xi, Z.; Plavec, J.; Zhou, C.
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'-SCF(3) -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:
DNA (5'-D(*CP*CP*AP*TP*(DSW)P*AP*TP*AP*GP*C)-3'), polymer, 10 residues, 3104.055 Da.
DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3'), polymer, 10 residues, 3084.041 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: 10160   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:

Experimental source:   Production method: chemical synthesis   Host organism: unidentified

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*CP*CP*AP*TP*(DSW)P*AP*TP*AP*GP*C)-3'): CCATXATAGC
DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3'): GCTATAATGG

Data sets:
Data typeCount
1H chemical shifts187

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 10 residues - 3104.055 Da.

1   DCDCDADT84EDADTDADGDC

Entity 2, entity_2 10 residues - 3084.041 Da.

1   DGDCDTDADTDADADTDGDG

Samples:

sample_1: DNA (5'-D(*CP*CP*AP*TP*(DSW)P*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; D2O, [U-2H], 100%

sample_2: DNA (5'-D(*CP*CP*AP*TP*(DSW)P*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; D2O, [U-2H], 10%; H2O 90%

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

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1anisotropicsample_conditions_1
2D 1H-1H NOESYsample_2anisotropicsample_conditions_1
2D DQF-COSYsample_1anisotropicsample_conditions_1
2D 1H-1H TOCSYsample_1anisotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

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

TopSpin, Bruker Biospin - chemical shift assignment

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

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

NMR spectrometers:

  • Bruker AVANCE NEO 600 MHz