2LIB | pdb_00002lib

DNA sequence context conceals alpha anomeric lesion

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	1-1 jump return	0.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 10 % D2O, 0.2 uM DSS, 2 mM EDTA	90% H2O/10% D2O	50	6.65	ambient	276
2	1D NOE	0.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 10 % D2O, 0.2 uM DSS, 2 mM EDTA	90% H2O/10% D2O	50	6.65	ambient	276
3	1-1 NOESY 2D 150 ms	0.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 10 % D2O, 0.2 uM DSS, 2 mM EDTA	90% H2O/10% D2O	50	6.65	ambient	276
4	Low Flip COSY	0.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 100 % D2O, 0.2 uM DSS, 2 mM EDTA	100% D2O	50		ambient	298
5	TOCYS	0.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 100 % D2O, 0.2 uM DSS, 2 mM EDTA	100% D2O	50		ambient	298
6	2D 1H 1H NOESY 75 ms	0.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 100 % D2O, 0.2 uM DSS, 2 mM EDTA	100% D2O	50		ambient	298
7	2D 1H 1H NOESY 125 ms	0.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 100 % D2O, 0.2 uM DSS, 2 mM EDTA	100% D2O	50		ambient	298
8	2D 1H-1H NOESY 250 ms	0.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 100 % D2O, 0.2 uM DSS, 2 mM EDTA	100% D2O	50		ambient	298
9	Constant Time COSY	0.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 100 % D2O, 0.2 uM DSS, 2 mM EDTA	100% D2O	50		ambient	298
10	2D 1H-13C HSQC	0.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 100 % D2O, 0.2 uM DSS, 2 mM EDTA	100% D2O	50		ambient	298
11	2D 1H-31P CORR	0.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 100 % D2O, 0.2 uM DSS, 2 mM EDTA	100% D2O	50		ambient	298
12	1D 31P	0.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 100 % D2O, 0.2 uM DSS, 2 mM EDTA	100% D2O	50		ambient	298

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

NMR Refinement
Method	Details	Software
restrained molecular dynamics	CORMA AMBER MARDIGRAS cycles with restrained molecular dynamics	Amber

NMR Ensemble Information
Conformer Selection Criteria	lowest AMBER violations
Conformers Calculated Total Number	10
Conformers Submitted Total Number	1
Representative Model	1 (lowest amber violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	Amber	9.0	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
2	chemical shift assignment	Sparky	3.3	Goddard
3	data analysis	TopSpin		Bruker Biospin
4	structure solution	CORMA		Thomas James
5	structure solution	MARDGIRAS		Thomas James
6	analysis	Curves	5.1	Richard Lavery
7	analysis	Curves	5.1	Heinz Sklenar
8	refinement	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm