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Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd position and 8-oxoguanine at the 10th position
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 50 mM sodium chloride, 10 mM potassium chloride, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') 100% D2O 120 mM 6.8 ambient 298 Bruker AVANCE III 600 2 2D 1H-1H NOESY 50 mM sodium chloride, 10 mM potassium chloride, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') 100% D2O 120 mM 6.8 ambient 278 Bruker AVANCE III 500 3 2D DQF-COSY 50 mM sodium chloride, 10 mM potassium chloride, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3') 100% D2O 120 mM 6.8 ambient 298 Bruker AVANCE III 500
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE III 500 2 Bruker AVANCE III 600
NMR Refinement Method Details Software simulated annealing Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 18 Conformers Submitted Total Number 12 Representative Model 1 (minimized average structure)
Computation: NMR Software # Classification Version Software Name Author 1 chemical shift assignment NMRView Johnson, One Moon Scientific 2 peak picking NMRView Johnson, One Moon Scientific 3 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 4 refinement Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 5 structure calculation Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman