5L06

Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd Position

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	50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')	100% D2O	120 mM	6.8	ambient	298	Varian INOVA 500
2	2D 1H-1H NOESY	50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')	100% D2O	120 mM	6.8	ambient	278	Varian INOVA 500
3	2D 1H-1H TOCSY	50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')	100% D2O	120 mM	6.8	ambient	298	Varian INOVA 500
4	2D DQF-COSY	50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')	100% D2O	120 mM	6.8	ambient	298	Varian INOVA 500

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	500

NMR Refinement
Method	Details	Software
simulated annealing		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	18
Conformers Submitted Total Number	9
Representative Model	1 (minimized average structure)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	chemical shift assignment	NMRView	9.0	Johnson, One Moon Scientific
2	peak picking	NMRView	9.0	Johnson, One Moon Scientific
3	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	data analysis	NMRView	9.0	Johnson, One Moon Scientific
5	data analysis	CYANA	2.1	Guntert, Mumenthaler and Wuthrich
6	refinement	Amber	12	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
8	structure calculation	Amber	12	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman