SOLUTION STRUCTURE OF THE DNA DUPLEX D(CCACCGGAAC).(GTTCCGGTGG) WITH A CHIRAL ALKYL-PHOSPHONATE MOIETY (DIAESTEREOISOMER R)
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 2mM duplex; 10mM phosphate, 100mM NaCl | 90% H20, 10% D2O | 7.0 | 1 atm | 278 | ||
| 2 | 2D NOESY | 2mM duplex; 10mM phosphate, 100mM NaCl | D2O | 7.0 | 1 atm | 298 | ||
| 3 | DQF-COSY | 2mM duplex; 10mM phosphate, 100mM NaCl | D2O | 7.0 | 1 atm | 298 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AMX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated, annealing molecular dynamics, matrix relaxation | the structures are based on a total of 280 NOE-derived distance constraints obtained from a complete relaxation matrix refinement. The structures were calculated by using restrained molecular dynamics with explicit solvent, and applying the particle mesh Ewald method. | MARDIGRAS |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | all calculated structures submitted |
| Conformers Calculated Total Number | 10 |
| Conformers Submitted Total Number | 10 |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | iterative matrix relaxation | MARDIGRAS | 5.2 | James, T.L. |
| 2 | refinement | Amber | 5.0 | Kollman, P.A. |
| 3 | collection | XwinNMR | 1.3 | Bruker |
