Human Telomeric DNA mixed-parallel/antiparallel quadruplex under Physiological Ionic Conditions Stabilized by Proper Incorporation of 8-Bromoguanosines
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 0.6mM DNA; 100mM KCl; 10mM K-phosphate (pH 6.3); 0.01mM DSS | 100% D2O | 110mM Potassium Ion | 6.3 | ambient | 298 | |
| 2 | 2D TOCSY | 0.6mM DNA; 100mM KCl; 10mM K-phosphate (pH 6.3); 0.01mM DSS | 100% D2O | 110mM Potassium Ion | 6.3 | ambient | 298 | |
| 3 | DQF-COSY | 0.6mM DNA; 100mM KCl; 10mM K-phosphate (pH 6.3); 0.01mM DSS | 100% D2O | 110mM Potassium Ion | 6.3 | ambient | 298 | |
| 4 | 2D NOESY | 0.6mM DNA; 100mM KCl; 10mM K-phosphate (pH 6.3); 0.01mM DSS, 95% H2O, 5% D2O | 95% H2O/5% D2O | 110mM Potassium Ion | 6.3 | ambient | 298 | |
| 5 | JR-HMBC | 1.3mM DNA; 100mM KCl; 10mM K-phosphate (pH 6.3); 0.01mM DSS, 95% H2O, 5% D2O | 95% H2O/5% D2O | 110mM Potassium Ion | 6.3 | ambient | 298 | |
| 6 | 13C-HSQC | 1.3mM DNA; 100mM KCl; 10mM K-phosphate (pH 6.3); 0.01mM DSS, 95% H2O, 5% D2O | 95% H2O/5% D2O | 110mM Potassium Ion | 6.3 | ambient | 298 | |
| 7 | H, P HSQC | 0.6mM DNA; 100mM KCl; 10mM K-phosphate (pH 6.3); 0.01mM DSS | 100% D2O | 110mM Potassium Ion | 6.3 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 800 |
| 2 | Bruker | AVANCE | 600 |
| 3 | Bruker | AVANCE | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | the structures are based on a total of 752 restraints, 582 are NOE-derived distance constraints, 110 dihedral angle restraints,48 distance restraints from hydrogen bonds, 12 planarity restraints for tetrad planes. | NMRPipe |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 1 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | NMRPipe | 2.4 | F. Delaglio |
| 2 | processing | XwinNMR | 3.5 | Bruker |
| 3 | data analysis | PIPP | 4.3.2 | D. Garrett |
| 4 | data analysis | Spaky | 3.112 | T.D. Goddard |
| 5 | structure solution | X-PLOR | 3.851 | A.T. Brunger |
| 6 | refinement | X-PLOR | 3.851 | A.T. Brunger |
