2N5P

Universal base control oligonucleotide structure

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 75 ms	1 mM DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), 100 % 100% Deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	100	6.79	ambient	294
2	2D Low Flip COSY	1 mM DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), 100 % 100% Deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	100	6.79	ambient	294
3	2D 1H-13C HSQC	1 mM DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), 100 % 100% Deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	100	6.79	ambient	294
4	2D 1H-1H constant time NOESY	1 mM DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), 100 % 100% Deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	100	6.79	ambient	294
5	2D 1H-1H TOCSY	1 mM DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), 100 % 100% Deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	100	6.79	ambient	294
6	2D 1H-31P CORR	1 mM DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), 100 % 100% Deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	100	6.79	ambient	294
7	1D 1H	1 mM DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), 100 % 100% Deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	100	6.79	ambient	294
8	1D 1H 1-1 jump and return	1 mM DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), 100 mM sodium chloride, 10 mM sodium phosphate, 90 % H2O, 10 % 100% deuterium D2O	90% H2O/10% D2O
9	1D 31P	1 mM DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), 100 % 100% Deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	100	6.79	ambient	294
10	2D 1H-1H NOESY 150 ms	1 mM DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), 100 % 100% Deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	100	6.79	ambient	294
11	2D 1H-1H NOESY 250 ms	1 mM DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), 100 % 100% Deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	100	6.79	ambient	294

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE	500

NMR Refinement
Method	Details	Software
molecular dynamics, matrix relaxation, distance geometry	AMBER 9 restrained MD simulations, MARDIGRAS, CORMA for comparisons of structure to NOE data (Rx values).	Amber

NMR Ensemble Information
Conformer Selection Criteria	back calculated data agree with experimental NOESY spectrum
Conformers Calculated Total Number	10
Conformers Submitted Total Number	1
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	Amber	9	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	refinement	Amber	9	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
3	chemical shift assignment	Sparky		Goddard
4	peak picking	Sparky		Goddard
5	collection	XwinNMR		Bruker Biospin
6	refinement	CORMA		Thomas James
7	data analysis	CORMA		Thomas James
8	data analysis	MARDIGRAS		Thomas James
9	refinement	MARDIGRAS		Thomas James