7YF7
NMR solution structures of the DNA minidumbbell formed by two ATTTT repeats
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 1 mM NA DNA (5'-D(*AP*TP*TP*TP*TP*AP*TP*TP*TP*T)-3'), 10 mM NA NaPi, 0.02 mM NA DSS | 99.96%D2O | 10 mM | 7 | 1 atm | 278 | Bruker AVANCE 500 |
2 | 2D 1H-1H COSY | 1 mM NA DNA (5'-D(*AP*TP*TP*TP*TP*AP*TP*TP*TP*T)-3'), 10 mM NA NaPi, 0.02 mM NA DSS | 99.96%D2O | 10 mM | 7 | 1 atm | 278 | Bruker AVANCE 500 |
4 | 2D 1H-1H TOCSY | 1 mM NA DNA (5'-D(*AP*TP*TP*TP*TP*AP*TP*TP*TP*T)-3'), 10 mM NA NaPi, 0.02 mM NA DSS | 99.96%D2O | 10 mM | 7 | 1 atm | 278 | Bruker AVANCE 500 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
2 | Bruker | AVANCE | 500 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 600 |
Conformers Submitted Total Number | 15 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | data analysis | TopSpin | Bruker Biospin | |
2 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |