2KUZ

2-Aminopurine incorporation perturbs the dynamics and structure of DNA

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-13C HMQC	3 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride	100% D2O		7.0	ambient	298
2	2D 1H-13C HMQC	3 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride, 20 mg/mL Pf1 phage	90% H2O/10% D2O		7.0	ambient	298
3	2D 1H-1H NOESY	3 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride	100% D2O		7.0	ambient	298
4	2D 1H-1H TOCSY	3 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride	100% D2O		7.0	ambient	298
5	2D DQF-COSY	3 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride	100% D2O		7.0	ambient	298
6	2D 1H-1H NOESY	3 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride	90% H2O/10% D2O		7.0	ambient	298

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

NMR Refinement
Method	Details	Software
simulated annealing	Torsion angle dynamics, 50K at 20,000K with subsequent gradual cooling to 25K in 154 steps of 0.5 ps length (34 steps to cool down to 3,000 K, followed by 120 steps to reach the end temperature) and a final minimization (3,000 steps).	CARA

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	11
Representative Model	1 (minimized average structure)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	peak picking	CARA	1.8.4	Keller, R. et al.
2	chemical shift assignment	CARA	1.8.4	Keller, R. et al.
3	structure solution	X-PLOR NIH	2.20	Schwieters, C. et al.
4	refinement	X-PLOR NIH	2.20	Schwieters, C. et al.
5	geometry optimization	X-PLOR NIH	2.20	Schwieters, C. et al.
6	collection	TopSpin	2.0	Bruker Biospin
7	processing	TopSpin	2.0	Bruker Biospin
8	data analysis	Gifa	4	Delsuc, M.A. et al.
9	data analysis	3DNA		Lu, X.J. et al.
10	data analysis	PALES		Zweckstetter, M. et al.