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Solution NMR structure of a 14-mer dsDNA complexed with a novel NIR fluorescent probe QCy-DT
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 300 uM DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3'), 300 uM QCY 90% H2O/10% D2O 10mM NaCl mM 7.0 1 atm 298 Bruker AVANCE III 700 2 2D 1H-1H TOCSY 300 uM DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3'), 300 uM QCY 90% H2O/10% D2O 10mM NaCl mM 7.0 1 atm 298 Bruker AVANCE III 700 3 2D DQF-COSY 300 uM DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3'), 300 uM QCY 90% H2O/10% D2O 10mM NaCl mM 7.0 1 atm 298 Bruker AVANCE III 700 4 2D 1H-1H NOESY 300 uM [U-2H] DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3'), 300 uM [U-2H] QCY 100% D2O 10mM NaCl mM 7.0 1 atm 298 Bruker AVANCE III 700 5 2D 1H-1H TOCSY 300 uM [U-2H] DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3'), 300 uM [U-2H] QCY 100% D2O 10mM NaCl mM 7.0 1 atm 298 Bruker AVANCE III 700 6 2D DQF-COSY 300 uM [U-2H] DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3'), 300 uM [U-2H] QCY 100% D2O 10mM NaCl mM 7.0 1 atm 298 Bruker AVANCE III 700
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE III 700
NMR Refinement Method Details Software torsion angle dynamics CYANA
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 20 Conformers Submitted Total Number 4 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 collection TopSpin Bruker Biospin 2 peak picking 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