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Solution structure of DNA duplex containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.5 M DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS 90% H2O/10% D2O 125 mM 7 1 atm 278 Bruker AVANCE 600 2 2D 1H-1H TOCSY 0.5 M DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS 90% H2O/10% D2O 125 mM 7 1 atm 278 Bruker AVANCE 600 3 2D 1H-1H COSY 0.5 mM DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS 100% D2O 125 mM 7 1 atm 298 Bruker AVANCE 600 4 2D 1H-1H NOESY 0.5 mM DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS 100% D2O 125 mM 7 1 atm 298 Bruker AVANCE 600 5 2D 1H-1H TOCSY 0.5 mM DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS 100% D2O 125 mM 7 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 all calculated structures submitted Conformers Calculated Total Number 10 Conformers Submitted Total Number 10 Representative Model 1 (fewest violations)
Computation: NMR Software # Classification Version Software Name Author 1 collection TopSpin Bruker Biospin 2 processing TopSpin Bruker Biospin 3 chemical shift assignment NMRFAM-SPARKY Goddard & Kneller 4 structure calculation Amber 18 Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 5 refinement Amber 18 Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 6 data analysis MOLMOL Koradi, Billeter and Wuthrich 7 data analysis 3DNA Lu & Olson