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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 19 Conformers Submitted Total Number 20 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