A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 200 micro-M DNA; 10mM potassium phosphate; 93% H2O/7% D2O | 93% H2O/7% D2O | 10 | 7.0 | ambient | 298 | |
| 2 | 2D 1H-1H TOCSY | 200 micro-M DNA; 10mM potassium phosphate; 93% H2O/7% D2O | 93% H2O/7% D2O | 10 | 7.0 | ambient | 298 | |
| 3 | 2D DQF-COSY | 200 micro-M DNA; 10mM potassium phosphate; 93% H2O/7% D2O | 93% H2O/7% D2O | 10 | 7.0 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 700 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, molecular dynamics | Explicit water refinement including potassium ions within the G-tetrads. | Sparky |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | chemical shift assignment | Sparky | Goddard | |
| 2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 3 | structure solution | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm | |
| 4 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm | |
