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NMR structure of 13mer duplex DNA containing an abasic site, averaged structure (alpha anomer)
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D NOESY 2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA 100% D2O 10 mM sodium phosphate mM 6.5 1 atm 298 2 2D TOCSY 2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA 100% D2O 10 mM sodium phosphate mM 6.5 1 atm 298 3 E-COSY 2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA 100% D2O 10 mM sodium phosphate mM 6.5 1 atm 298 4 H-P-selective HSQC 2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA 100% D2O 10 mM sodium phosphate mM 6.5 1 atm 298 5 2D NOESY 2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA 90% H2O/10% D2O(v/v) 10 mM sodium phosphate mM 6.5 1 atm 277
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Home-built Custom-built 750 2 Home-built Custom-built 591
NMR Refinement Method Details Software simulated annealing
matrix relaxation the structures are based on 482 NOE-derived distance constraints, 57 dihedral angle restraints,8 distance restraints
from hydrogen bonds. Amber
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 30 Conformers Submitted Total Number 1 Representative Model 1 (minimized average structure)
Additional NMR Experimental Information Details This structure was determined using standard 2D homonuclear and HP-HSQC techniques
Computation: NMR Software # Classification Version Software Name Author 1 data analysis Felix 2000 2 geometry optimization MARDIGRAS 3 refinement Amber 8.0 Case, et al.