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Structure of perimidinone-derived synthetic nucleoside paired with guanine in DNA duplex
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.53 mM 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate 100% D2O 100 7.0 ambient 283 2 2D 1H-1H COSY 0.53 mM 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate 100% D2O 100 7.0 ambient 283 3 2D 1H-1H NOESY 0.53 mM 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', 10 mM sodium phosphate, 50 uM EDTA, 100 mM sodium chloride 90% H2O/10% D2O 100 7.0 ambient 278
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 800 2 Bruker AVANCE 600
NMR Refinement Method Details Software simulated annealing Amber
NMR Ensemble Information Conformer Selection Criteria back calculated data agree with experimental NOESY spectrum Conformers Calculated Total Number 10 Conformers Submitted Total Number 10 Representative Model 1 (minimized average structure)
Computation: NMR Software # Classification Version Software Name Author 1 refinement Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman 2 collection TopSpin Bruker Biospin 3 processing TopSpin Bruker Biospin 4 data analysis CORMA Thomas L. James 5 data analysis Curves 5.3 Ravishankar, G. et al. 6 processing MARDIGRAS Thomas L. James 7 chemical shift assignment Sparky Goddard 8 chemical shift calculation Sparky Goddard