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Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 1.1 mM 11 mer duplex oligo B-D, 25 mM phosphate buffer, 50 mM NaCl, 0.5 mM EDTA 100% D2O 6.8 ambient 298 2 2D 1H-1H COSY 1.1 mM 11 mer duplex oligo B-D, 25 mM phosphate buffer, 50 mM NaCl, 0.5 mM EDTA 100% D2O 6.8 ambient 298 3 2D DQF-COSY 1.1 mM 11 mer duplex oligo B-D, 25 mM phosphate buffer, 50 mM NaCl, 0.5 mM EDTA 100% D2O 6.8 ambient 298 4 2D 1H-1H TOCSY 1.1 mM 11 mer duplex oligo B-D, 25 mM phosphate buffer, 50 mM NaCl, 0.5 mM EDTA 100% D2O 6.8 ambient 298 5 2D 1H-13C HSQC 1.1 mM 11 mer duplex oligo B-D, 25 mM phosphate buffer, 50 mM NaCl, 0.5 mM EDTA 100% D2O 6.8 ambient 298 6 2D 1H-1H NOESY 1.1 mM 11 mer duplex oligo B-D, 25 mM phosphate buffer, 50 mM NaCl, 0.5 mM EDTA 90% H2O/10% D2O 6.8 ambient 278
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 800
NMR Refinement Method Details Software molecular dynamics TopSpin
NMR Ensemble Information Conformer Selection Criteria all calculated structures submitted Conformers Calculated Total Number 6 Conformers Submitted Total Number 7 Representative Model 1 (minimized average structure)
Computation: NMR Software # Classification Version Software Name Author 1 collection TopSpin Bruker Biospin 2 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 3 chemical shift assignment Sparky Goddard 4 data analysis Sparky Goddard 5 peak picking Sparky Goddard 6 peak volume calc. Sparky Goddard 7 geometry optimization X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 8 refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 9 structure solution X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore