6IJW | pdb_00006ijw

SOLUTION NMR STRUCTURE OF A DODECAMERIC dsDNA COMPLEXED WITH A NIR FLUORESCENT PROBE QCy-DT

SOLUTION NMR

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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*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*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*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*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*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*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
5	structure calculation	CYANA	2.1	Guntert, Mumenthaler and Wuthrich
6	geometry optimization	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman