Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.3 mM RNA (34-MER)-1, 0.26 mM [U-100% 13C; U-100% 15N] RNA (34-MER)-2 | 100% D2O | 50 | 6.5 | ambient | 288 | |
| 2 | 2D 1H-1H TOCSY | 0.3 mM RNA (34-MER)-1, 0.26 mM [U-100% 13C; U-100% 15N] RNA (34-MER)-2 | 100% D2O | 50 | 6.5 | ambient | 288 | |
| 3 | 2D 1H-13C HSQC | 0.3 mM RNA (34-MER)-1, 0.26 mM [U-100% 13C; U-100% 15N] RNA (34-MER)-2 | 100% D2O | 50 | 6.5 | ambient | 288 | |
| 4 | 2D 1H-13C HSQC | 0.3 mM RNA (34-MER)-1, 0.26 mM [U-100% 13C; U-100% 15N] RNA (34-MER)-2 | 100% D2O | 50 | 6.5 | ambient | 288 | |
| 5 | 2D 1H-13C HSQC | 0.18 mM [U-13C; U-15N]-Ade RNA (34-MER)-3, 0.19 mM [U-13C; U-15N]-Gua RNA (34-MER)-4 | 95% H2O/5% D2O | 50 | 6.5 | ambient | 288 | |
| 6 | 2D 1H-13C TROSY | 0.3 mM RNA (34-MER)-1, 0.26 mM [U-100% 13C; U-100% 15N] RNA (34-MER)-2 | 100% D2O | 50 | 6.5 | ambient | 288 | |
| 7 | 2D 1H-13C TROSY | 0.3 mM RNA (34-MER)-1, 0.26 mM [U-100% 13C; U-100% 15N] RNA (34-MER)-2 | 100% D2O | 50 | 6.5 | ambient | 288 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| 2 | Bruker | DRX | 600 |
| 3 | Bruker | AVANCE | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | TopSpin | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 200 |
| Conformers Submitted Total Number | 11 |
| Representative Model | 1 (minimized average structure) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | TopSpin | 2.1 | Bruker Biospin |
| 2 | processing | TopSpin | 2.1 | Bruker Biospin |
| 3 | structure solution | CNSSOLVE | 1.3 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 4 | refinement | CNSSOLVE | 1.3 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 5 | peak picking | Sparky | 3.114 | Goddard |
| 6 | grid search | X-PLOR NIH | 2.32 | Schwieters, Kuszewski, Tjandra and Clore |
