7E4E
NMR solution structures of DNA minidumbbell containing a N1-methyladenine
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 | 0.5 mM NA DNA (5'-D(*TP*TP*TP*(MA7)P*TP*TP*TP*A)-3'), 10 mM NA sodium phosphate, 0.02 mM NA DSS | 99.96% D2O | 10 mM | 7.0 | 1 atm | 278 | Bruker AVANCE 500 |
2 | 2D DQF-COSY | 0.5 mM NA DNA (5'-D(*TP*TP*TP*(MA7)P*TP*TP*TP*A)-3'), 10 mM NA sodium phosphate, 0.02 mM NA DSS | 99.96% D2O | 10 mM | 7.0 | 1 atm | 278 | Bruker AVANCE 500 |
3 | 2D 1H-1H TOCSY | 0.5 mM NA DNA (5'-D(*TP*TP*TP*(MA7)P*TP*TP*TP*A)-3'), 10 mM NA sodium phosphate, 0.02 mM NA DSS | 99.96% D2O | 10 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 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 5 |
Representative Model | 1 (fewest violations) |
Computation: NMR Software | ||||
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# | 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 |