2MS9
Solution structure of a G-quadruplex
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H JR NOESY | 0.2-2 mM DNA (28-MER)-1, 0.2-0.5 mM [U-2% 15N] DNA (28-MER)-2, 0.2-0.5 mM [U-100% 2H] DNA (28-MER)-3 | 90% H2O/10% D2O | 90 | 7 | 298 | ||
2 | 2D 1H-1H NOESY | 0.2-2 mM DNA (28-MER)-4, 0.2-1 mM [U-4% 13C; U-4% 15N] DNA (28-MER)-5 | 100% D2O | 90 | 7 | 298 | ||
3 | 2D 1H-1H TOCSY | 0.2-2 mM DNA (28-MER)-4, 0.2-1 mM [U-4% 13C; U-4% 15N] DNA (28-MER)-5 | 100% D2O | 90 | 7 | 298 | ||
4 | 2D 1H-13C HSQC aliphatic | 0.2-2 mM DNA (28-MER)-4, 0.2-1 mM [U-4% 13C; U-4% 15N] DNA (28-MER)-5 | 100% D2O | 90 | 7 | 298 | ||
5 | 2D 1H-13C HSQC aromatic | 0.2-2 mM DNA (28-MER)-4, 0.2-1 mM [U-4% 13C; U-4% 15N] DNA (28-MER)-5 | 100% D2O | 90 | 7 | 298 | ||
6 | 2D 1H-13C JR HMBC | 0.2-2 mM DNA (28-MER)-1, 0.2-0.5 mM [U-2% 15N] DNA (28-MER)-2, 0.2-0.5 mM [U-100% 2H] DNA (28-MER)-3 | 90% H2O/10% D2O | 90 | 7 | 298 | ||
7 | 15N-FILTERED | 0.2-2 mM DNA (28-MER)-1, 0.2-0.5 mM [U-2% 15N] DNA (28-MER)-2, 0.2-0.5 mM [U-100% 2H] DNA (28-MER)-3 | 90% H2O/10% D2O | 90 | 7 | 298 | ||
8 | D-LABELED | 0.2-2 mM DNA (28-MER)-1, 0.2-0.5 mM [U-2% 15N] DNA (28-MER)-2, 0.2-0.5 mM [U-100% 2H] DNA (28-MER)-3 | 90% H2O/10% D2O | 90 | 7 | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Bruker | AVANCE | 700 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
DGSA-distance geometry simulated annealing, Distance-restrained molecular dynamics | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
2 | data analysis | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | data analysis | Sparky | Goddard | |
5 | peak picking | Sparky | Goddard | |
6 | collection | TopSpin | Bruker Biospin | |
7 | geometry optimization | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
8 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore |