2L8C
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1 - UU pair with zero hydrogen bond pairs
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D DQF-COSY | 1.5 mM RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3') | 100% D2O | 0.1 | 7.2 | ambient | 313 | |
2 | 2D 1H-1H NOESY | 1.5 mM RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3') | 100% D2O | 0.1 | 7.2 | ambient | 313 | |
3 | 2D 1H-1H TOCSY | 1.5 mM RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3') | 100% D2O | 0.1 | 7.2 | ambient | 313 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 500 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
molecular dynamics | CYANA |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with acceptable covalent geometry |
Conformers Calculated Total Number | 25 |
Conformers Submitted Total Number | 1 |
Representative Model | 1 (fewest violations) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | geometry optimization | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
2 | chemical shift assignment | Sparky | 3.111 | Goddard |
3 | data analysis | Sparky | 3.111 | Goddard |
4 | peak picking | Sparky | 3.111 | Goddard |
5 | refinement | Amber | 11 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |
6 | structure solution | Amber | 11 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |