5KIF

Structural impact of single ribonucleotides in DNA

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY 250 ms	1 mM DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 100 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	110 mM	6.6	ambient atm	294	Bruker AVANCE 600
2	2D NOESY	1 mM DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 10 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	90% H2O/10% D2O	110 mM	7.0	ambient atm	294	Bruker AVANCE 600
3	2D Low Flip COSY	1 mM DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 100 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	110 mM	6.6	ambient atm	294	Bruker AVANCE 600
4	2D 1H-13C HSQC	1 mM DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 100 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	110 mM	6.6	ambient atm	294	Bruker AVANCE III 850
5	2D constant time NOESY	1 mM DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 100 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	110 mM	6.6	ambient atm	294	Bruker AVANCE 600
6	2D 1H-31P CORR	1 mM DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 100 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	110 mM	6.6	ambient atm	294	Bruker AVANCE 600
7	2D NOESY 150 ms	1 mM DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 100 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	110 mM	6.6	ambient atm	294	Bruker AVANCE 600
10	1D 1H	1 mM DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 100 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	110 mM	6.6	ambient atm	294	Bruker AVANCE 600
9	1D 31P	1 mM DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 100 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	100% D2O	110 mM	6.6	ambient atm	294	Bruker AVANCE 600
8	1D 1H 1-1 jump and return	1 mM DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 10 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate	90% H2O/10% D2O	110 mM	7.0	ambient atm	294	Bruker AVANCE 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE III	850

NMR Refinement
Method	Details	Software
matrix relaxation, molecular dynamics		MARDIGRAS

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	8
Conformers Submitted Total Number	3
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure calculation	Amber	9	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	chemical shift assignment	Sparky	3.33	Goddard
3	collection	TopSpin		Bruker Biospin
4	refinement	CORMA		Thomas James
5	refinement	MARDIGRAS		Thomas James