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An i-motif domain able to undergo pH-dependent conformational transitions (acidic structure)
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H TOCSY 500 uM DNA (5'-D(*CP*(DNR)P*GP*TP*TP*(DNR)P*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*(DNR)P*CP*GP*T)-3'), 10 mM sodium phosphate, 0.5 v/v DSS 90% H2O/10% D2O 10 mM 5 1 atm 278 Bruker AVANCE 600 2 2D 1H-1H TOCSY 500 uM DNA (5'-D(*CP*(DNR)P*GP*TP*TP*(DNR)P*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*(DNR)P*CP*GP*T)-3'), 10 mM sodium phosphate, 0.5 v/v DSS 90% H2O/10% D2O 10 mM 5 1 atm 298 Bruker AVANCE 600 3 2D 1H-1H TOCSY 500 uM DNA (5'-D(*CP*(DNR)P*GP*TP*TP*(DNR)P*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*(DNR)P*CP*GP*T)-3'), 10 mM sodium phosphate, 0.5 v/v DSS 100% D2O 10 mM 5 1 atm 298 Bruker AVANCE 600 4 2D 1H-1H NOESY 500 uM DNA (5'-D(*CP*(DNR)P*GP*TP*TP*(DNR)P*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*(DNR)P*CP*GP*T)-3'), 10 mM sodium phosphate, 0.5 v/v DSS 90% H2O/10% D2O 10 mM 5 1 atm 278 Bruker AVANCE 600 5 2D 1H-1H NOESY 500 uM DNA (5'-D(*CP*(DNR)P*GP*TP*TP*(DNR)P*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*(DNR)P*CP*GP*T)-3'), 10 mM sodium phosphate, 0.5 v/v DSS 90% H2O/10% D2O 10 mM 5 1 atm 298 Bruker AVANCE 600 6 2D 1H-1H NOESY 500 uM DNA (5'-D(*CP*(DNR)P*GP*TP*TP*(DNR)P*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*(DNR)P*CP*GP*T)-3'), 10 mM sodium phosphate, 0.5 v/v DSS 100% D2O 10 mM 5 1 atm 298 Bruker AVANCE 600 7 2D DQF-COSY 500 uM DNA (5'-D(*CP*(DNR)P*GP*TP*TP*(DNR)P*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*(DNR)P*CP*GP*T)-3'), 10 mM sodium phosphate, 0.5 v/v DSS 100% D2O 10 mM 5 1 atm 298 Bruker AVANCE 600
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600
NMR Refinement Method Details Software molecular dynamics Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 15 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 collection TopSpin Bruker Biospin 2 processing TopSpin Bruker Biospin 3 chemical shift assignment Sparky Goddard 4 structure calculation CYANA Guntert, Mumenthaler and Wuthrich 5 refinement Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 6 data analysis 3DNA Lu and Olson 7 data analysis MOLMOL Koradi, Billeter and Wuthrich