Structure and Stability of Duplex DNA Containing (5'S) 5',8-Cyclo-2'-Deoxyadenosine: An Oxidative Lesion Repair by NER
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.7 mM 11 mer DNA duplex | 100% D2O | 6.7 | ambient | 298 | ||
| 2 | 2D 1H-1H COSY | 0.7 mM 11 mer DNA duplex | 100% D2O | 6.7 | ambient | 298 | ||
| 3 | 2D 1H-1H TOCSY | 0.7 mM 11 mer DNA duplex | 100% D2O | 6.7 | ambient | 298 | ||
| 4 | 2D 1H-15N HSQC | 0.7 mM 11 mer DNA duplex | 100% D2O | 6.7 | ambient | 298 | ||
| 5 | 2D 1H-1H NOESY | 0.7 mM 11 mer DNA duplex | 90% H2O/10% D2O | 6.7 | ambient | 278 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| 2 | Bruker | AVANCE | 400 |
| 3 | Bruker | AVANCE | 700 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | VNMR | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | all calculated structures submitted |
| Conformers Calculated Total Number | 26 |
| Conformers Submitted Total Number | 26 |
| Representative Model | 1 (minimized average structure) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VNMR | Varian | |
| 2 | collection | TopSpin | Bruker Biospin | |
| 3 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 4 | processing | Felix | Accelrys Software Inc. | |
| 5 | peak picking | Sparky | Goddard | |
| 6 | chemical shift assignment | Sparky | Goddard | |
| 7 | data analysis | Sparky | Goddard | |
| 8 | geometry optimization | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 9 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 10 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 11 | geometry optimization | HYPER | Tejero, Monleon, Celda, Powers and Montelione | |
| 12 | data analysis | HYPER | Tejero, Monleon, Celda, Powers and Montelione | |
| 13 | data analysis | Insight II | Accelrys Software Inc. | |
