2M1V

NMR solution structure of the d3'-hairpin from the Sc.ai5gamma group II intron including the EBS1:dIBS1 RNA:DNA hybrid

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	0.6-0.9 mM RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
2	2D 1H-1H TOCSY	0.6-0.9 mM RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
3	2D 1H-1H NOESY	0.6-0.9 mM [3',4',5',5'',5]-100% 2H RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
4	2D 1H-1H NOESY	0.5-1.0 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
5	2D 1H-1H TOCSY	0.5-1.0 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
6	2D 1H-15N HSQC	0.6-0.9 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	298
7	2D 1H-15N HSQC	0.6-0.9 mM RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	278
8	2D 1H-13C HSQC aliphatic	0.6-0.9 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
9	2D 1H-13C HSQC aromatic	0.6-0.9 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
10	2D 1H-1H NOESY	0.6-0.9 mM RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	293
11	2D 1H-1H NOESY	0.6-0.9 mM RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	278
12	2D 1H-13C HSQC aliphatic	0.6-0.9 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
13	2D 1H-13C HSQC aromatic	0.6-0.9 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
14	1D 31P	0.6-0.9 mM RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
15	F1, F2 X-filtered 1H-1H NOESY	0.6-0.9 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	298
16	F1, F2 X-filtered 1H-1H TOCSY	0.6-0.9 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	700
2	Bruker	AVANCE	600
3	Bruker	AVANCE	500

NMR Refinement
Method	Details	Software
molecular dynamics, torsion angle dynamics		TopSpin

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	200
Conformers Submitted Total Number	18
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	TopSpin	3.0	Bruker Biospin
2	data analysis	TopSpin	3.0	Bruker Biospin
3	data analysis	Sparky		Goddard
4	chemical shift assignment	Sparky		Goddard
5	peak picking	Sparky		Goddard
6	data analysis	DYANA	1.5	Guntert, Braun and Wuthrich
7	structure solution	DYANA	1.5	Guntert, Braun and Wuthrich
8	structure solution	CNS	1.2	Brunger, Adams, Clore, Gros, Nilges and Read
9	structure solution	X-PLOR NIH	2.3	Schwieters, Kuszewski, Tjandra and Clore
10	refinement	X-PLOR NIH	2.3	Schwieters, Kuszewski, Tjandra and Clore