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 | 0.7 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3'), 0.7 mM 4-guanidinophenyl 4-guanidinobenzoate, 5 mM potassium phosphate, 0.25 mM EDTA | 100% D2O | 5 mM | 6.0 | 1 atm | 298 | Bruker AVANCE III 700 |
| 2 | 2D DQF-COSY | 0.7 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3'), 0.7 mM 4-guanidinophenyl 4-guanidinobenzoate, 5 mM potassium phosphate, 0.25 mM EDTA | 100% D2O | 5 mM | 6.0 | 1 atm | 298 | Bruker AVANCE III 700 |
| 3 | 2D NOESY | 0.7 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3'), 0.7 mM 4-guanidinophenyl 4-guanidinobenzoate, 5 mM potassium phosphate, 0.25 mM EDTA | 95% H2O/5% D2O | 5 mM | 6.0 | 1 atm | 279 | Bruker AVANCE III 700 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | 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 (2008) SPARKY 3. University of California, San Francisco. |
