NCSi-gb-bulge-DNA complex induced formation of a DNA bulge structure by a molecular wedge ligand-post-activated neocarzinostatin chromophore
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 90% H2O, 10% D2O | 90% H2O/10% D2O | 0.1M NACL, 10 mM SODIUM PHOSPHATE | 6.4 | 270 | ||
| 2 | 2D NOESY | ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 99.96% D2O | 99.96% D2O | 0.1M NACL, 10 mM SODIUM PHOSPHATE | 6.4 | 278 | ||
| 3 | DQF-COSY | ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 99.96% D2O | 99.96% D2O | 0.1M NACL, 10 mM SODIUM PHOSPHATE | 6.4 | 278 | ||
| 4 | PE-COSY | ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 99.96% D2O | 99.96% D2O | 0.1M NACL, 10 mM SODIUM PHOSPHATE | 6.4 | 278 | ||
| 5 | TOCSY, H-P COSY | ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 99.96% D2O | 99.96% D2O | 0.1M NACL, 10 mM SODIUM PHOSPHATE | 6.4 | 278 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AMX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| distance geometry (DG), restrained molecular dynamics (rMDS), and relaxation matrix refinement | A total of 681 NMR restraints is used to derive the final refined structures. The total restraints consist of 590 of NOE-derived distance restraints and 91 of dihedral angle restraints. Especially, 85 of intermolecular distance restraints are derived which represent the interaction between the drug and the bulge duplex. | X-PLOR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | all calculated structures submitted |
| Conformers Calculated Total Number | 7 |
| Conformers Submitted Total Number | 7 |
| Additional NMR Experimental Information | |
|---|---|
| Details | This structure was determined using 2D homonuclear and heteronuclear techniques |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | X-PLOR | 3.01 | Brunger |
