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Tetrameric i-motif structure of dT-dC-dC-CFL-CFL-dC at acidic pH
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.5-2.0 mM DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3'), 10 mM sodium chloride 90% H2O/10% D2O 10 5.0 1 atm 278 2 2D 1H-1H NOESY 0.5-2.0 mM DNA/RNA (5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(TAF)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3'), 10 mM sodium chloride 100% D2O 10 5.0 1 atm 298 3 2D DQF-COSY 0.5-2.0 mM DNA/RNA (5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(TAF)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3'), 10 mM sodium chloride 100% D2O 10 5.0 1 atm 298 4 2D 1H-1H TOCSY 0.5-2.0 mM DNA/RNA (5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(TAF)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3'), 10 mM sodium chloride 100% D2O 10 5.0 1 atm 298 5 2D 1H-19F HOESY 0.5-2.0 mM DNA/RNA (5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(TAF)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3'), 10 mM sodium chloride 100% D2O 10 5.0 1 atm 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600 2 Bruker AVANCE 800 3 Bruker AVANCE 700
NMR Refinement Method Details Software molecular dynamics Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 20 Conformers Submitted Total Number 10 Representative Model 1 (closest to the average)
Computation: NMR Software # Classification Version Software Name Author 1 geometry optimization Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman 2 data analysis MOLMOL Koradi, Billeter and Wuthrich 3 peak picking Sparky Goddard 4 refinement Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman