Solution NMR structure of quadruplex d(TGGGTTTGGGTTGGGTTTGGG) in sodium conditions
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H TOCSY | 5-6 mM D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3', 20 mM sodium phosphate, 70 mM sodium chloride | 100% D2O | 95 | 6.8 | ambient | 293 | |
| 2 | 2D 1H-1H DQF-COSY | 5-6 mM D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3', 20 mM sodium phosphate, 70 mM sodium chloride | 100% D2O | 95 | 6.8 | ambient | 293 | |
| 3 | 2D 1H-1H NOESY | 5-6 mM D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3', 20 mM sodium phosphate, 70 mM sodium chloride | 100% D2O | 95 | 6.8 | ambient | 293 | |
| 4 | 2D 1H-1H NOESY | 5-6 mM D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3', 20 mM sodium phosphate, 70 mM sodium chloride | 93% H2O/7% D2O | 95 | 6.8 | ambient | 278 | |
| 5 | 2D 1H-31P HSQC | 5-6 mM D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3', 20 mM sodium phosphate, 70 mM sodium chloride | 100% D2O | 95 | 6.8 | ambient | 293 | |
| 6 | 2D 1H-13C HMBC (H1-H8 long range correlation) | 5-6 mM D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3', 20 mM sodium phosphate, 70 mM sodium chloride | 93% H2O/7% D2O | 95 | 6.8 | ambient | 278 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | VNMRS 500 | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| DGSA-distance geometry simulated annealing, molecular dynamics | VnmrJ | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 50 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VnmrJ | Varian | |
| 2 | processing | Felix | Accelrys Software Inc. | |
| 3 | chemical shift assignment | Felix | Accelrys Software Inc. | |
| 4 | data analysis | Felix | Accelrys Software Inc. | |
| 5 | chemical shift assignment | Sparky | Goddard | |
| 6 | data analysis | Sparky | Goddard | |
| 7 | data analysis | MOLMOL | Koradi, Billeter and Wuthrich | |
| 8 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 9 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
