Solution Structure of DNA Containing Alpha-OH-PdG: the Mutagenic Adduct Produced by Acrolein
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 2.5 mM DNA duplex, alpha-OH-PdG-1 | 100% D2O | 50mM NaCl | 5.9 | ambient | 298 | |
| 2 | 2D 1H-1H TOCSY | 2.5 mM DNA duplex, alpha-OH-PdG-1 | 100% D2O | 50mM NaCl | 5.9 | ambient | 298 | |
| 3 | 2D 1H-1H COSY | 2.5 mM DNA duplex, alpha-OH-PdG-1 | 100% D2O | 50mM NaCl | 5.9 | ambient | 298 | |
| 4 | 2D DQF-COSY | 2.5 mM DNA duplex, alpha-OH-PdG-1 | 100% D2O | 50mM NaCl | 5.9 | ambient | 298 | |
| 5 | 2D 1H-1H NOESY | 2.5 mM DNA duplex, alpha-OH-PdG-2 | 90% H2O/10% D2O | 50mM NaCl | 5.9 | ambient | 278 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| restrained molecular dynamics | Felix | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | all calculated structures submitted |
| Conformers Calculated Total Number | 25 |
| Conformers Submitted Total Number | 26 |
| Representative Model | 1 (minimized average) |
| Additional NMR Experimental Information | |
|---|---|
| Details | AUTHOR STATES THAT 25 MODELS WERE CALCULATED BY RESTRAINED MD. MODEL 1 IS AN AVERAGED MINIMIZED STRUCTURE OF THESE 25 MODELS. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | Felix | Accelrys Software Inc. | |
| 2 | data analysis | Felix | Accelrys Software Inc. | |
| 3 | chemical shift assignment | Felix | Accelrys Software Inc. | |
| 4 | peak picking | Felix | Accelrys Software Inc. | |
| 5 | collection | VNMR | Varian | |
| 6 | geometry optimization | Insight II | Accelrys Software Inc. | |
| 7 | geometry optimization | Chimera | UCSF Chimera | |
| 8 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 9 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
