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Solution Structure of DNA Dodecamer with 8-oxoguanine at 4th 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, 1 mM EDTA, 0.2 mM DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3') 100% D2O 120 mM 6.8 ambient 298 Bruker AVANCE 700 2 2D 1H-1H NOESY 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 0.2 mM DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3') 100% D2O 120 mM 6.8 ambient 278 Bruker AVANCE 700 3 2D DQF-COSY 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 0.2 mM DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3') 100% D2O 120 mM 6.8 ambient 298 Bruker AVANCE 700 5 2D 1H-1H TOCSY 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 0.2 mM DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3') 100% D2O 120 mM 6.8 ambient 298 Bruker AVANCE 700 4 31P HETCOR 50 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 0.2 mM DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*CP*GP*CP*G)-3') 100% D2O 120 mM 6.8 ambient 298 Bruker AVANCE 700
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 700
NMR Refinement Method Details Software simulated annealing Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 20 Conformers Submitted Total Number 14 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 7 structure calculation Amber 12 Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman