NMR structures of small molecules bound to a model of an RNA CAG repeat expansion
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 0.4 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3'), 0.6 mM 4-[(3-methoxyphenyl)amino]-2-methylquinoline-6-carboximidamide, 5 mM potassium, 0.5 mM EDTA | 95% H2O/5% D2O | 5 mM | 6.0 | 1 atm | 308 | Bruker AVANCE III HD 900 |
| 2 | 2D DQF-COSY | 0.4 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3'), 0.6 mM 4-[(3-methoxyphenyl)amino]-2-methylquinoline-6-carboximidamide, 5 mM potassium, 0.5 mM EDTA | 95% H2O/5% D2O | 5 mM | 6.0 | 1 atm | 308 | Bruker AVANCE III HD 900 |
| 3 | 2D NOESY | 0.4 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3'), 0.6 mM 4-[(3-methoxyphenyl)amino]-2-methylquinoline-6-carboximidamide, 5 mM potassium, 0.5 mM EDTA | 95% H2O/5% D2O | 5 mM | 6.0 | 1 atm | 282 | Bruker AVANCE III 700 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III HD | 900 |
| 2 | Bruker | AVANCE III | 700 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (fewest violations) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | TopSpin | Bruker Biospin | |
| 2 | structure calculation | Amber | 20 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman |
| 3 | data analysis | NMRFAM-SPARKY | 1.470 | Goddard TD, Kneller DG |
