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NMR Structure of a 1:1 Complex of Polyamide (Im-Py-Beta-Im-Beta-Im-Py-Beta-Dp) with the Tridecamer DNA Duplex 5'-CCAAAGAGAAGCG-3'
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D NOESY 3.67 millimolar polyamide-DNA complex, 10 millimolar sodium phosphate, pH 7.0, 90% H2O, 10% D2O 90% H2O/10% D2O 10 Millimolar 7.0 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian INOVA 600
NMR Refinement Method Details Software restrained molecular dynamics/simulated annealing, matrix relaxation/NOE-derived distance restraints. The structure calculations used 548 distance restraints. 508 were NOE-derived, and 40 were for Watson-Crick hydrogen bonds. VNMR
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 40 Conformers Submitted Total Number 11 Representative Model 1 (fewest violations)
Additional NMR Experimental Information Details This structure was determined using standard 2D homonuclear techniques.
Computation: NMR Software # Classification Version Software Name Author 1 collection VNMR 6.1 B Varian Associates, Inc. 2 processing NMRPipe 1 Delalgio, grzesiek, Vuister, Zhu, Pfeifer, & Bax 3 data analysis NMRView 4.1.2 Johnson, & Blevins 4 iterative matrix relaxation MARDIGRAS 3.2 Borgias, & James 5 structure solution Amber 6.0 Kollman, Case, Merz, Cheatham, Simmerling, Darden, Pearlman, Caldwell, Ross, Ferguson, Seibel, Singh, & Weiner 6 refinement SANDER MODULE OF AMBER 6.0 PACKAGE (2000) Kollman, Case, Merz, Cheatham, Simmerling, Darden, Pearlman, Caldwell, Ross, Ferguson, Seibel, Singh, & Weiner