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Structure and dynamics of a DNA GNRA hairpin solved vy high-sensitivity NMR with two independent converging methods, simulated annealing (DYANA) and mesoscopic molecular modelling (BCE/AMBER)
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D DQF-COSY
4 mM dGCGAAAGC, 10 mM sodium phosphate, 0.0025 mM sodium azide, 0.005 mM EDTA, 50 mM sodium chloride
100% D2O
50
6.8
ambient
298
2
2D 1H-13C HSQC
4 mM dGCGAAAGC, 10 mM sodium phosphate, 0.0025 mM sodium azide, 0.005 mM EDTA, 50 mM sodium chloride
100% D2O
50
6.8
ambient
298
3
2D 1H-31P COSY
4 mM dGCGAAAGC, 10 mM sodium phosphate, 0.0025 mM sodium azide, 0.005 mM EDTA, 50 mM sodium chloride
100% D2O
50
6.8
ambient
298
4
2D 1H-1H NOESY
4 mM dGCGAAAGC, 10 mM sodium phosphate, 0.0025 mM sodium azide, 0.005 mM EDTA, 50 mM sodium chloride
100% D2O
50
6.8
ambient
298
5
2D 1H-1H NOESY
4 mM dGCGAAAGC, 10 mM sodium phosphate, 0.0025 mM sodium azide, 0.005 mM EDTA, 50 mM sodium chloride
100 structures were used in DYANA simulated annealing approach to give models 1 to 20 that were energy-refined with AMBER, Model number 21 was constructed with the BCE approach in agreement with the NMR data and then energy-refined with AMBER