Structure and dynamics of RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.5 mM NA Adenosine, Cytidine,Guanosine, Uridine RNA (5'-R(*GP*AP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*C)-3'), 5.0 mM potassium phosphate, 0.25 mM EDTA | 100% D2O | 0.0112 M | 6 | 1 atm | 298 | Bruker Avance III HD UltraShield 700 |
| 2 | 2D 1H-1H NOESY | 0.5 uM NA Adenosine, Cytidine,Guanosine, Uridine RNA (5'-R(*GP*AP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*C)-3'), 5.0 mM potassium phosphate, 0.25 nM EDTA | 90% H2O/10% D2O | 0.0112 M | 6 | 1 atm | 276 | Bruker Avance III HD Ascend 850 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | Avance III HD UltraShield | 700 |
| 2 | Bruker | Avance III HD Ascend | 850 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 40 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | TopSpin | 3.5 | Bruker Biospin |
| 2 | refinement | Amber | 16 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
| 3 | chemical shift assignment | Sparky | 3.0 | Goddard |
| 4 | peak picking | Sparky | 3.0 | Goddard |
| 5 | data analysis | Amber | 16 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
| 6 | processing | NMRPipe | 8.9 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
| 7 | structure calculation | Amber | 16 | |
