Solution structure of a G-quadruplex
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H JR NOESY | 0.2-2 mM DNA (28-MER)-1, 0.2-0.5 mM [U-2% 15N] DNA (28-MER)-2, 0.2-0.5 mM [U-100% 2H] DNA (28-MER)-3 | 90% H2O/10% D2O | 90 | 7 | 298 | ||
| 2 | 2D 1H-1H NOESY | 0.2-2 mM DNA (28-MER)-4, 0.2-1 mM [U-4% 13C; U-4% 15N] DNA (28-MER)-5 | 100% D2O | 90 | 7 | 298 | ||
| 3 | 2D 1H-1H TOCSY | 0.2-2 mM DNA (28-MER)-4, 0.2-1 mM [U-4% 13C; U-4% 15N] DNA (28-MER)-5 | 100% D2O | 90 | 7 | 298 | ||
| 4 | 2D 1H-13C HSQC aliphatic | 0.2-2 mM DNA (28-MER)-4, 0.2-1 mM [U-4% 13C; U-4% 15N] DNA (28-MER)-5 | 100% D2O | 90 | 7 | 298 | ||
| 5 | 2D 1H-13C HSQC aromatic | 0.2-2 mM DNA (28-MER)-4, 0.2-1 mM [U-4% 13C; U-4% 15N] DNA (28-MER)-5 | 100% D2O | 90 | 7 | 298 | ||
| 6 | 2D 1H-13C JR HMBC | 0.2-2 mM DNA (28-MER)-1, 0.2-0.5 mM [U-2% 15N] DNA (28-MER)-2, 0.2-0.5 mM [U-100% 2H] DNA (28-MER)-3 | 90% H2O/10% D2O | 90 | 7 | 298 | ||
| 7 | 15N-FILTERED | 0.2-2 mM DNA (28-MER)-1, 0.2-0.5 mM [U-2% 15N] DNA (28-MER)-2, 0.2-0.5 mM [U-100% 2H] DNA (28-MER)-3 | 90% H2O/10% D2O | 90 | 7 | 298 | ||
| 8 | D-LABELED | 0.2-2 mM DNA (28-MER)-1, 0.2-0.5 mM [U-2% 15N] DNA (28-MER)-2, 0.2-0.5 mM [U-100% 2H] DNA (28-MER)-3 | 90% H2O/10% D2O | 90 | 7 | 298 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| 2 | Bruker | AVANCE | 700 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| DGSA-distance geometry simulated annealing, Distance-restrained molecular dynamics | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
| 2 | data analysis | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 3 | chemical shift assignment | Sparky | Goddard | |
| 4 | data analysis | Sparky | Goddard | |
| 5 | peak picking | Sparky | Goddard | |
| 6 | collection | TopSpin | Bruker Biospin | |
| 7 | geometry optimization | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 8 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
