2N3M
G-quadruplex structure of an anti-proliferative DNA sequence
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 1.2-2 mM DNA (28-MER)-1 | 90% H2O/10% D2O | 90 | 7 | 298 | ||
2 | 2D 1H-1H NOESY | 1.2-2 mM DNA (28-MER)-3 | 100% D2O | 90 | 7 | 298 | ||
3 | 2D 1H-13C HSQC | 1.2-2 mM DNA (28-MER)-3 | 100% D2O | 90 | 7 | 298 | ||
4 | 2D 1H-1H TOCSY | 1.2-2 mM DNA (28-MER)-3 | 100% D2O | 90 | 7 | 298 | ||
5 | 1D 15N-Filtered | 0.2-1 mM [U-2% 15N] DNA (28-MER)-2 | 90% H2O/10% D2O | 90 | 7 | 298 | ||
6 | 1D D-labeled | 0.2-1 mM [U-100% 2H] DNA (28-MER)-4 | 100% 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 | ||
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Method | Details | Software |
DGSA-distance geometry simulated annealing | Amber |
NMR Ensemble Information | |
---|---|
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 | structure solution | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
3 | geometry optimization | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
4 | geometry optimization | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
5 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
6 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
7 | chemical shift assignment | Sparky | Goddard | |
8 | data analysis | Sparky | Goddard | |
9 | peak picking | Sparky | Goddard | |
10 | collection | TopSpin | Bruker Biospin |