Structures of small molecules bound to RNA repeat expansions that cause Huntington's disease-like 2 and myotonic dystrophy type 1
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 0.3 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 0.6 mM 1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-ium, 5 mM potassium phosphate, 0.25 mM EDTA | 100% D2O | 5 mM | 6.0 | 1 atm | 308 | Bruker AVANCE III HD 700 |
| 2 | 2D DQF-COSY | 0.3 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 0.6 mM 1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-ium, 5 mM potassium phosphate, 0.25 mM EDTA | 100% D2O | 5 mM | 6.0 | 1 atm | 308 | Bruker AVANCE III HD 700 |
| 3 | 2D NOESY | 0.3 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 0.6 mM 1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-ium, 5 mM potassium phosphate, 0.25 mM EDTA | 95% H2O/5% D2O | 10 mM | 6.0 | 1 atm | 278 | Bruker AVANCE III HD 850 |
| 4 | 2D NOESY | 0.3 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 0.6 mM 1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-ium, 5 mM potassium phosphate, 0.25 mM EDTA | 95% H2O/5% D2O | 5 mM | 6.0 | 1 atm | 288 | Bruker AVANCE III HD 850 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III HD | 700 |
| 2 | Bruker | AVANCE III HD | 850 |
| 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 | processing | TopSpin | 3.5 | Bruker Biospin |
| 2 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
| 3 | chemical shift assignment | NMRFAM-SPARKY | 1.3 | Bioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12 NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Lee W, Tonelli M, Markley JL |
| 4 | peak picking | NMRFAM-SPARKY | 1.3 | Bioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12 NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Lee W, Tonelli M, Markley JL |
