2KQG
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 |