☰ Navigation Tabs
Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd 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 phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') 100% D2O 120 mM 6.8 ambient 298 Varian INOVA 500 2 2D 1H-1H NOESY 50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') 100% D2O 120 mM 6.8 ambient 278 Varian INOVA 500 3 2D 1H-1H TOCSY 50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') 100% D2O 120 mM 6.8 ambient 298 Varian INOVA 500 4 2D DQF-COSY 50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') 100% D2O 120 mM 6.8 ambient 298 Varian INOVA 500
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian INOVA 500
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 9 Representative Model 1 (minimized average structure)
Computation: NMR Software # Classification Version Software Name Author 1 chemical shift assignment NMRView 9.0 Johnson, One Moon Scientific 2 peak picking NMRView 9.0 Johnson, One Moon Scientific 3 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 4 data analysis NMRView 9.0 Johnson, One Moon Scientific 5 data analysis CYANA 2.1 Guntert, Mumenthaler and Wuthrich 6 refinement Amber 12 Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 8 structure calculation Amber 12 Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman