5IZP
Solution Structure of DNA Dodecamer with 8-oxoguanine at 10th Position
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') | 100% D2O | 120 mM | 6.8 | ambient | 298 | Bruker AVANCE 700 |
| 2 | 2D 1H-1H NOESY | 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') | 90% H2O/10% D2O | 120 mM | 6.8 | ambient | 278 | Bruker AVANCE 700 |
| 3 | 2D 1H-1H TOCSY | 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') | 100% D2O | 120 mM | 6.8 | ambient | 298 | Bruker AVANCE 700 |
| 4 | 2D DQF-COSY | 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') | 100% D2O | 120 mM | 6.8 | ambient | 298 | Bruker AVANCE 700 |
| 5 | 2D 1H-31P HETCOR | 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') | 100% D2O | 120 mM | 6.8 | ambient | 298 | Bruker AVANCE 700 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 700 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 18 |
| Conformers Submitted Total Number | 15 |
| Representative Model | 1 (minimized average structure) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | Amber | 12 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman |
| 2 | structure calculation | Amber | 12 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman |
| 3 | chemical shift assignment | NMRView | 9 | Johnson, One Moon Scientific |
| 4 | peak picking | NMRView | 9 | Johnson, One Moon Scientific |
| 5 | data analysis | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 6 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 7 | data analysis | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
