NMR reveals absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 2.5 mM RNA | 90% H2O/10% D2O | 80 | 6 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 500 |
| 2 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, molecular dynamics | CNS | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy and least distance and angle violations |
| Conformers Calculated Total Number | 20 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure solution | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
| 2 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 3 | chemical shift assignment | Sparky | Goddard | |
| 4 | data analysis | Sparky | Goddard | |
| 5 | peak picking | Sparky | Goddard | |
| 6 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 7 | refinement | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
