2M53

G-rich VEGF aptamer with LNA modifications

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	0.5 mM DNA(25-MER)-7, 10 mM potassium phosphate-8, 90 mM potassium chloride-9	100% D2O	100	7.0	ambient	298
2	2D DQF-COSY	0.5 mM DNA(25-MER)-7, 10 mM potassium phosphate-8, 90 mM potassium chloride-9	100% D2O	100	7.0	ambient	298
3	2D 1H-1H TOCSY	0.5 mM DNA(25-MER)-7, 10 mM potassium phosphate-8, 90 mM potassium chloride-9	100% D2O	100	7.0	ambient	298
4	2D 1H-1H NOESY	0.5 mM DNA(25-MER)-1, 10 mM potassium phosphate-2, 90 mM potassium chloride-3	90% H2O/10% D2O	100	7.0	ambient	298
5	2D 1H-1H NOESY	0.5 mM DNA(25-MER)-4, 10 mM potassium phosphate-5, 40 mM potassium chloride-6	90% H2O/10% D2O	50	7.0	ambient	298
6	2D 1H-1H NOESY	0.5 mM DNA(25-MER)-1, 10 mM potassium phosphate-2, 90 mM potassium chloride-3	90% H2O/10% D2O	100	7.0	ambient	273

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	VNMRS	600
2	Varian	VNMRS	800

NMR Refinement
Method	Details	Software
simulated annealing		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	Amber	11	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	refinement	Amber	11	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
3	data analysis	Amber	11	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
4	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5	chemical shift assignment	Sparky		Goddard
6	peak picking	Sparky		Goddard
7	collection	VnmrJ		Agilent Technologies