NMR Solution Structures of +3 (5' staggered) Bistranded Abasic Site Lesions in DNA
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | unknown mM DNA (5'-D(*CP*AP*GP*CP*GP*(3DR)P*GP*TP*AP*TP*AP*AP*GP*C)-3'), unknown mM DNA (5'-D(*GP*CP*TP*TP*AP*(3DR)P*AP*CP*AP*CP*GP*CP*TP*G)-3') | 100% D2O | 6.8 | ambient | 298 | ||
| 2 | 2D 1H-1H COSY | unknown mM DNA (5'-D(*CP*AP*GP*CP*GP*(3DR)P*GP*TP*AP*TP*AP*AP*GP*C)-3'), unknown mM DNA (5'-D(*GP*CP*TP*TP*AP*(3DR)P*AP*CP*AP*CP*GP*CP*TP*G)-3') | 100% D2O | 6.8 | ambient | 298 | ||
| 3 | 2D DQF-COSY | unknown mM DNA (5'-D(*CP*AP*GP*CP*GP*(3DR)P*GP*TP*AP*TP*AP*AP*GP*C)-3'), unknown mM DNA (5'-D(*GP*CP*TP*TP*AP*(3DR)P*AP*CP*AP*CP*GP*CP*TP*G)-3') | 100% D2O | 6.8 | ambient | 298 | ||
| 4 | 2D 1H-1H TOCSY | unknown mM DNA (5'-D(*CP*AP*GP*CP*GP*(3DR)P*GP*TP*AP*TP*AP*AP*GP*C)-3'), unknown mM DNA (5'-D(*GP*CP*TP*TP*AP*(3DR)P*AP*CP*AP*CP*GP*CP*TP*G)-3') | 100% D2O | 6.8 | ambient | 298 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics, DGSA-distance geometry simulated annealing | Authors indicate chirality error at DT8 in model 1 due to flexibility of the DNA duplex in solution | X-PLOR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 20 |
| Conformers Submitted Total Number | 4 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | geometry optimization | X-PLOR | 3.1 | Brunger |
| 2 | refinement | X-PLOR | 3.1 | Brunger |
