8X4F
Solution NMR structure of a DNA hairpin formed by pure CTG repeats
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 0.5 mM DNA (5'-D(*GP*CP*TP*GP*CP*TP*GP*CP*TP*GP*CP*TP*GP*C)-3'), 0.02 mM DSS, 1 mM sodium phosphate | 99.96%D2O | 1 mM | 7.0 | 1 atm | 288 | Bruker AVANCE NEO 600 |
2 | 2D 1H-1H TOCSY | 0.5 mM DNA (5'-D(*GP*CP*TP*GP*CP*TP*GP*CP*TP*GP*CP*TP*GP*C)-3'), 0.02 mM DSS, 1 mM sodium phosphate | 99.96%D2O | 1 mM | 7.0 | 1 atm | 288 | Bruker AVANCE NEO 600 |
3 | 2D 1H-1H COSY | 0.5 mM DNA (5'-D(*GP*CP*TP*GP*CP*TP*GP*CP*TP*GP*CP*TP*GP*C)-3'), 0.02 mM DSS, 1 mM sodium phosphate | 99.96%D2O | 1 mM | 7.0 | 1 atm | 288 | Bruker AVANCE NEO 600 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE NEO | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 500 |
Conformers Submitted Total Number | 5 |
Representative Model | 1 (fewest violations) |
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 |