2M11

Structure of perimidinone-derived synthetic nucleoside paired with guanine in DNA duplex

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	0.53 mM 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate	100% D2O	100	7.0	ambient	283
2	2D 1H-1H COSY	0.53 mM 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate	100% D2O	100	7.0	ambient	283
3	2D 1H-1H NOESY	0.53 mM 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', 10 mM sodium phosphate, 50 uM EDTA, 100 mM sodium chloride	90% H2O/10% D2O	100	7.0	ambient	278

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	Avance	800
2	Bruker	Avance	600

NMR Refinement
Method	Details	Software
simulated annealing		AMBER

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

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	AMBER		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	collection	TOPSPIN		Bruker Biospin
3	processing	TOPSPIN		Bruker Biospin
4	data analysis	CORMA		Thomas L. James
5	data analysis	CURVES	5.3	Ravishankar, G. et al.
6	processing	MARDIGRAS		Thomas L. James
7	chemical shift assignment	SPARKY		Goddard
8	chemical shift calculation	SPARKY		Goddard