BMRB Entry 25840

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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/BMR25840
MolProbity Validation Chart

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Title:
Tetrameric i-motif structure of dT-dC-dC-CFL-CFL-dC at acidic pH
Deposition date:
2015-10-09
Original release date:
2016-08-15
Authors:
Abou-Assi, Robert; Harkness, Robert; Martin-Pintado, Nerea; Wilds, Christopher; Campos-Olivas, Ramon; Mittermaier, Anthony; Gonzalez, Carlos; Damha, Masad
Citation:

Citation: Abou-Assi, Hala; Harkness, Robert; Martin-Pintado, Nerea; Wilds, Christopher; Campos-Olivas, Ramon; Mittermaier, Anthony; Gonzalez, Carlos; Damha, Masad. "Stabilization of i-motif structures by 2'-beta-fluorination of DNA"  Nucleic Acids Res. 44, 4998-5009 (2016).
PubMed: 27166371

Assembly members:

Assembly members:
DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3'), polymer, 6 residues, 1741.139 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3'): TCCXXC

Data sets:
Data typeCount
1H chemical shifts51

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_11
2DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_21
3DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_31
4DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_41

Entities:

Entity 1, DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_1 6 residues - 1741.139 Da.

1   DTDCDCCFLCFLDC

Samples:

sample_1: DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3') 1.25 mM; sodium chloride 10 mM

sample_2: DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3') 1.25 mM; sodium chloride 10 mM

sample_conditions_1: ionic strength: 10 mM; pH: 5.0; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 10 mM; pH: 5.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D DQF-COSYsample_2isotropicsample_conditions_2
2D 1H-1H TOCSYsample_2isotropicsample_conditions_2
2D 1H-19F HOESYsample_2isotropicsample_conditions_2

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - geometry optimization

Molmol, Koradi, Billeter and Wuthrich - data analysis

SPARKY, Goddard - peak picking

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 700 MHz