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NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, 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 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 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
Molecular dynamics 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,structures with the lowest energy Conformers Calculated Total Number 30 Conformers Submitted Total Number 10 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 refinement Amber 8.0 Case, D.A. et al. 2 data analysis Felix 2000 3 geometry optimization MARDIGRAS