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
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Title: Tetrameric i-motif structure of dT-dC-dC-CFL-CFL-dC at acidic pH PubMed: 27166371
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: 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).
Assembly members:
DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3'), polymer, 6 residues, 1741.139 Da.
Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3'): TCCXXC
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 51 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_1 | 1 |
| 2 | DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_2 | 1 |
| 3 | DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_3 | 1 |
| 4 | DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_4 | 1 |
Entities:
Entity 1, DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_1 6 residues - 1741.139 Da.
| 1 | DT | DC | DC | CFL | CFL | DC |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_2 |
| 2D DQF-COSY | sample_2 | isotropic | sample_conditions_2 |
| 2D 1H-1H TOCSY | sample_2 | isotropic | sample_conditions_2 |
| 2D 1H-19F HOESY | sample_2 | isotropic | sample_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