Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 11mer DNA duplex with MeC5 and [BP]G6 modified | H2O and D2O | 100 mM NaCl | 6.8 | 1 atm | 273 | |
| 2 | 2D TOCSY | 11mer DNA duplex with MeC5 and [BP]G6 modified | H2O and D2O | 100 mM NaCl | 6.8 | 1 atm | 273 | |
| 3 | DQF-COSY | 11mer DNA duplex with MeC5 and [BP]G6 modified | H2O and D2O | 100 mM NaCl | 6.8 | 1 atm | 273 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing molecular dynamics matrix relaxation | X-PLOR | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function |
| Conformers Calculated Total Number | 9 |
| Conformers Submitted Total Number | 9 |
| Representative Model | 1 (fewest violations,lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | X-PLOR | 3.1 | Brunger |
