Solution NMR structure of a RNA duplex formed by C9orf72 GGGGCC repeats
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.5 mM RNA (5'-R(*CP*CP*GP*GP*GP*GP*CP*CP*GP*G)-3'), 1 mM sodium phosphate, 0.02 mM DSS, 100 mM sodium chloride | 99.96% D2O | 101 mM | 7.0 | 1 atm | 283 | Bruker AVANCE 600 |
| 3 | 2D 1H-1H NOESY | 0.5 mM RNA (5'-R(*CP*CP*GP*GP*GP*GP*CP*CP*GP*G)-3'), 1 mM sodium phosphate, 0.02 mM DSS, 100 mM sodium chloride | 90% H2O/10% D2O | 101 mM | 7.0 | 1 atm | 278 | Bruker AVANCE 600 |
| 2 | 2D 1H-1H COSY | 0.5 mM RNA (5'-R(*CP*CP*GP*GP*GP*GP*CP*CP*GP*G)-3'), 1 mM sodium phosphate, 0.02 mM DSS, 100 mM sodium chloride | 99.96% D2O | 101 mM | 7.0 | 1 atm | 283 | Bruker AVANCE 600 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | GROMACS | |
| refinement | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 200 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (closest to the average) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | chemical shift assignment | TopSpin | Biospin | |
| 2 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
| 3 | structure calculation | GROMACS | 2021.7 | Alekseenko, Apol, Apostolov, Bauer, Berendsen, Bjelkmar, Blau, ... and Hess |
