6I4O
Dodecamer DNA containing the synthetic base pair P-Z
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 | 1.3 mM ZP-DNA | 100% D2O | 100 mM | 7.5 | 1 atm | 298 | Bruker AVANCE II 600 |
2 | 2D DQF-COSY | 1.3 mM ZP-DNA | 100% D2O | 100 mM | 7.5 | 1 atm | 298 | Bruker AVANCE II 600 |
3 | 2D 1H-1H TOCSY | 1.3 mM ZP-DNA | 100% D2O | 100 mM | 7.5 | 1 atm | 298 | Bruker AVANCE II 600 |
4 | 2D 1H-13C HSQC | 1.3 mM ZP-DNA | 100% D2O | 100 mM | 7.5 | 1 atm | 298 | Bruker AVANCE II 600 |
5 | 2D 1H-1H NOESY | 1.3 mM ZP-DNA | 90% H2O/10% D2O | 100 mM | 7.5 | 1 atm | 298 | Bruker AVANCE II 600 |
6 | 2D 31P-1H COSY | 1.3 mM ZP-DNA | 100% D2O | 100 mM | 7.5 | 1 atm | 298 | Bruker AVANCE II 600 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE II | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | Amber | |
molecular dynamics | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | clustering of MD |
Conformers Calculated Total Number | 5000 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (most represented cluster) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | chemical shift assignment | Sparky | Goddard | |
2 | processing | TopSpin | Bruker | |
4 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
5 | refinement | MARDIGRAS | Brandan A. Borgias Paul D. Thomas He Liu Anil Kumar | |
6 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |