2-Hydroxy-7-nitrofluorene covalently linked into a 13mer DNA duplex - solution structure of the face-down orientation
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H COSY | 3 mM Strand I-6, 3 mM Strand II-7, 10 mM sodium phosphate-8, 150 mM sodium chloride-9 | 100% D2O | 7 | ambient | 298 | ||
| 2 | 2D 1H-1H NOESY | 3 mM Strand I-6, 3 mM Strand II-7, 10 mM sodium phosphate-8, 150 mM sodium chloride-9 | 100% D2O | 7 | ambient | 298 | ||
| 3 | 2D 1H-1H NOESY | 3 mM Strand I-10, 3 mM Strand II-11, 10 mM sodium phosphate-12, 150 mM sodium chloride-13 | 90% H2O/10% D2O | 7 | ambient | 298 | ||
| 4 | 2D 1H-13C HSQC | 3 mM Strand I-6, 3 mM Strand II-7, 10 mM sodium phosphate-8, 150 mM sodium chloride-9 | 100% D2O | 7 | ambient | 298 | ||
| 5 | 2D 1H-13C HSQC_decoupled | 3 mM Strand I-6, 3 mM Strand II-7, 10 mM sodium phosphate-8, 150 mM sodium chloride-9 | 100% D2O | 7 | ambient | 298 | ||
| 6 | 2D 1H-13C HSQC_decoupled | 3 mM Strand I-1, 3 mM Strand II-2, 20 mg/mL Pf1 phage-3, 10 mM sodium phosphate-4, 150 mM sodium chloride-5 | 100% D2O | 7 | ambient | 298 | ||
| 7 | 2D 1H-1H TOCSY | 3 mM Strand I-6, 3 mM Strand II-7, 10 mM sodium phosphate-8, 150 mM sodium chloride-9 | 100% D2O | 7 | ambient | 298 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, torsion angle dynamics | Gifa | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 11 |
| Representative Model | 1 (minimized average) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | data analysis | Gifa | 4 | Delsuc |
| 2 | geometry optimization | X-PLOR NIH | 2.20 | Schwieters, Kuszewski, Tjandra and Clore |
| 3 | refinement | X-PLOR NIH | 2.20 | Schwieters, Kuszewski, Tjandra and Clore |
| 4 | structure solution | X-PLOR NIH | 2.21 | Schwieters, Kuszewski, Tjandra and Clore |
| 5 | data analysis | CARA | 1.8.4 | Rochus T. Keller |
| 6 | peak picking | CARA | 1.8.4 | Rochus T. Keller |
| 7 | collection | TopSpin | 2.1 | Bruker Biospin |
| 8 | processing | TopSpin | 2.1 | Bruker Biospin |
