DNA containing a cluster of 8-oxo-guanine and abasic site lesion: beta anomer (6AP, 8OG14)
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.88 mM DNA (5'-D(*CP*GP*CP*TP*CP*(AAB)P*CP*AP*CP*GP*C)-3'), 0.88 mM DNA (5'-D(*GP*CP*(8OG)P*TP*GP*GP*GP*AP*GP*CP*G)-3') | 100% D2O | 120 | 6 | ambient | 283 | |
| 2 | 2D DQF-COSY | 0.88 mM DNA (5'-D(*CP*GP*CP*TP*CP*(AAB)P*CP*AP*CP*GP*C)-3'), 0.88 mM DNA (5'-D(*GP*CP*(8OG)P*TP*GP*GP*GP*AP*GP*CP*G)-3') | 100% D2O | 120 | 6 | ambient | 283 | |
| 3 | 2D 1H-1H TOCSY | 0.88 mM DNA (5'-D(*CP*GP*CP*TP*CP*(AAB)P*CP*AP*CP*GP*C)-3'), 0.88 mM DNA (5'-D(*GP*CP*(8OG)P*TP*GP*GP*GP*AP*GP*CP*G)-3') | 100% D2O | 120 | 6 | ambient | 283 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | UNITYPLUS | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, molecular dynamics | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 500 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (closest to the average) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure solution | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman | |
| 2 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman | |
