Solution Structure of cis-5R,6S-thymine glycol opposite complementary guanine in duplex DNA
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 20 mM sodium phosphate-1, 100 mM sodium chloride-2, 10 uM sodium azide-3, 50 uM EDTA-4 | 100% D2O | 0.1 | 7.0 | ambient | 303 | |
| 2 | 2D 1H-1H COSY | 20 mM sodium phosphate-1, 100 mM sodium chloride-2, 10 uM sodium azide-3, 50 uM EDTA-4 | 100% D2O | 0.1 | 7.0 | ambient | 303 | |
| 3 | 2D 1H-1H NOESY | 20 mM sodium phosphate-5, 100 mM sodium chloride-6, 10 uM sodium azide-7, 50 uM EDTA-8 | 90% H2O/10% D2O | 0.1 | 7.0 | ambient | 278 | |
| 4 | 2D 31P-1H COSY | 20 mM sodium phosphate-1, 100 mM sodium chloride-2, 10 uM sodium azide-3, 50 uM EDTA-4 | 100% D2O | 0.1 | 7.0 | ambient | 303 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 800 |
| 2 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, molecular dynamics | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | back calculated data agree with experimental NOESY spectrum |
| Conformers Calculated Total Number | 10 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (closest to the average) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm | |
| 2 | chemical shift assignment | Sparky | Goddard | |
| 3 | data analysis | Sparky | Goddard | |
| 4 | processing | TopSpin | Bruker Biospin | |
| 5 | restraint generation | MARDIGRAS | Borgias, B.A. & James, T.L. | |
| 6 | structure validation | CORMA | James T.L. | |
| 7 | data analysis | Curves | Lavery, R. and Sklenar, H | |
| 8 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
