6M0B
Solution NMR structures of DNA minidumbbell formed by 5'-CTTG CGTG-3'.
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
2 | 2D 1H-1H NOESY | 1 mM DNA (5'-D(*CP*TP*TP*GP*CP*GP*TP*G)-3'), 10 mM sodium phosphate, 0.02 mM DSS | 99.96% D2O | 10 NaPi mM | 7.0 | 1 atm | 278 | Bruker AVANCE 700 |
3 | 2D DQF-COSY | 1 mM DNA (5'-D(*CP*TP*TP*GP*CP*GP*TP*G)-3'), 10 mM sodium phosphate, 0.02 mM DSS | 99.96% D2O | 10 NaPi mM | 7.0 | 1 atm | 278 | Bruker AVANCE 700 |
4 | 2D 1H-1H TOCSY | 1 mM DNA (5'-D(*CP*TP*TP*GP*CP*GP*TP*G)-3'), 10 mM sodium phosphate, 0.02 mM DSS | 99.96% D2O | 10 NaPi mM | 7.0 | 1 atm | 278 | Bruker AVANCE 500 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 500 |
2 | Bruker | AVANCE | 700 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 500 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | chemical shift assignment | TopSpin | Bruker Biospin | |
2 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
3 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |