NMR Structure of a 21 bp DNA duplex preferentially cleaved by Human Topoisomerase II
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 46mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 90% H2O/10% D2O | 90% H2O/10% D2O | 0.1 | 7.00 | 1 atm | 303 | |
| 2 | 2D 1H-1H NOESY | 46mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 100% D2O | 100% D2O | 0.1 | 7.00 | 1 atm | 303 | |
| 3 | 2D DQF-COSY | 46mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 100% D2O | 100% D2O | 0.1 | 7.00 | 1 atm | 303 | |
| 4 | 2D 1H-1H TOCSY | 46mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 100% D2O | 100% D2O | 0.1 | 7.00 | 1 atm | 303 | |
| 5 | 2D 1H-13C HSQC | 46mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 100% D2O | 100% D2O | 0.1 | 7.00 | 1 atm | 303 | |
| 6 | 2D 1H-31P HETCOR | 46mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 100% D2O | 100% D2O | 0.1 | 7.00 | 1 atm | 303 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| SIMULATED ANNEALING, MOLECULAR DYNAMICS | THE STRUCTURE IS BASED ON A TOTAL OF 670 NOE, 102 HYDROGEN BOND, AND 286 DIHEDRAL RESTRAINTS | X-PLOR NIH |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 50 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | X-PLOR NIH | 2.16 | Schwieters, Kuszewski, Tjandra and Clore |
| 2 | data analysis | MORASS | 2.51 | Luxon |
