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AG repetition attached to a compact i-motif clip at 3'-end
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 1.3 mM AGAGCCC 90% H2O/10% D2O 60 mM 5 1 atm 278 Bruker AVANCE III HD 700 2 2D 1H-1H NOESY 1.3 mM AGAGCCC 100% D2O 60 mM 5 1 atm 288 Bruker AVANCE III HD 700
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE III HD 700
NMR Refinement Method Details Software molecular dynamics In total, 1 microsecond of unrestrained MD in explicit solvent. Trajectory after 300 ns discarded due to partial disruption of NMR-derived structure. Amber
NMR Ensemble Information Conformer Selection Criteria Snapshot every 100 nanoseconds taken from initial 300 ns of 1 microsecond unrestrained MD. Conformers Calculated Total Number 3000 Conformers Submitted Total Number 4 Representative Model 1 (minimized average structure)
Computation: NMR Software # Classification Version Software Name Author 1 refinement Amber 16 Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 2 structure calculation Amber 16 Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 3 chemical shift assignment NMRFAM-SPARKY 1.413 Nuclear Magnetic Resonance Facility at Madison 4 collection TopSpin 4 Bruker Biospin