Solution structure of DNA duplex containing N3T-ethylene-N1I interstrand cross-link
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.5 mM 5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3', 0.5 mM 5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3', 0.5 mM ethane | 100% D2O | 0.1 | 7.5 | ambient | 298 | |
| 2 | 2D 1H-1H TOCSY | 0.5 mM 5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3', 0.5 mM 5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3', 0.5 mM ethane | 100% D2O | 0.1 | 7.5 | ambient | 298 | |
| 3 | 2D DQF-COSY | 0.5 mM 5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3', 0.5 mM 5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3', 0.5 mM ethane | 100% D2O | 0.1 | 7.5 | ambient | 298 | |
| 4 | 2D 1H-31P HSQC | 0.5 mM 5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3', 0.5 mM 5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3', 0.5 mM ethane | 100% D2O | 0.1 | 7.5 | ambient | 298 | |
| 5 | 2D 1H-1H NOESY | 0.5 mM 5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3', 0.5 mM 5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3', 0.5 mM ethane | 90% H2O/10% D2O | 0.1 | 7.5 | ambient | 273 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | Unity Inova | 500 |
| 2 | Varian | VNMRS | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | CNS | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations and the lowest energy |
| Conformers Calculated Total Number | 25 |
| Conformers Submitted Total Number | 11 |
| Representative Model | 1 (minimized average structure) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 3 | data analysis | NMRView | Johnson, One Moon Scientific | |
| 4 | collection | VnmrJ | Varian | |
