NMR Solution Structure of an In Vitro Selected RNA which is Sequence Specifically Recognized by Hamster Nucleolin RBD12.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 1 mM sNRE 2-5 mM Na+ added for pH | 10% D2O 90% H2O, pH=6.0 | low (2-5 mM added Na+) | 6 | ambient | 278 | |
| 2 | H-N HMQC | 0.5 mM U-13C/15N sNRE 2-5 mM Na+ added for pH | 10 D2O 90% H2O | low (2-5 mM added Na+) | 6 | ambient | 278 | |
| 3 | 2D NOESY | 1 mM sNRE 2-5 mM Na+ added for pH | 99.99% D2O | low (2-5 mM added Na+) | 6 | ambient | 303 | |
| 4 | 3D_13C-separated_NOESY | 0.5 mM U-13C/15N sNRE 2-5 mM Na+ added for pH | 99.99% D2O | low (2-5 mM added Na+) | 6 | ambient | 303 | |
| 5 | HCCH TOCSY | 0.5 mM U-13C/15N sNRE 2-5 mM Na+ added for pH | 99.99% D2O | low (2-5 mM added Na+) | 6 | ambient | 303 | |
| 6 | DQF-COSY | 1 mM sNRE 2-5 mM Na+ added for pH | 99.99% D2O | low (2-5 mM added Na+) | 6 | ambient | 303 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 500 |
| 2 | Bruker | DRX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Simulated annealing starting from randomized templates. Base planarity restraints were added. | XwinNMR | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | all calculated structures submitted |
| Conformers Calculated Total Number | 18 |
| Conformers Submitted Total Number | 18 |
| Representative Model | 18 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | RNA was also assigned using U/C, A, and, G specifically labeled samples. Dieckmann, T., Feigon, J. J. Biomol. NMR 9 (1997) 259-272. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | 2.6 | Bruker |
| 2 | processing | XwinNMR | 2.6 | Bruker |
| 3 | data analysis | Felix | 97.0 | Molecular Simulations Inc. |
| 4 | structure solution | X-PLOR | 3.8 | Brunger & Nilges |
| 5 | refinement | X-PLOR | 3.8 | Brunger & Nilges |
