An unexpected mode of small molecule DNA binding provides the structural basis for DNA cleavage by the potent antiproliferative agent (-)-lomaiviticin A
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D DQF-COSY | 1.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A | 100% D2O | 24 | 7.5 | ambient | 297 | |
| 2 | 2D 1H-13C HSQC | 1.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A | 100% D2O | 24 | 7.5 | ambient | 297 | |
| 3 | 2D 1H-1H NOESY | 1.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A | 100% D2O | 24 | 7.5 | ambient | 297 | |
| 4 | 2D 1H-1H NOESY | 1.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A | 100% D2O | 24 | 7.5 | ambient | 297 | |
| 5 | 2D 1H-1H NOESY | 1.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A | 90% H2O/10% D2O | 24 | 7.5 | ambient | 297 | |
| 6 | 2D DQF-COSY | 1.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A | 90% H2O/10% D2O | 24 | 7.5 | ambient | 297 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Agilent | Direct Drive | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 1000 |
| Conformers Submitted Total Number | 6 |
| Representative Model | 1 (minimized average structure) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure calculation | Amber | 14 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman |
| 2 | refinement | Amber | 14 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman |
