5KIB

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(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-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(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3'), 100 mM sodium chloride, 10 mM sodium phosphate, 10 % 100% deuterium D2O	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(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-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(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-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(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-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(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-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	2D NOESY 150 ms	1 mM DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-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 1H	1 mM DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-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 31P	1 mM DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-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	1D 1H 1-1 jump and return	1 mM DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3'), 100 mM sodium chloride, 10 mM sodium phosphate, 10 % 100% deuterium D2O	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	back calculated data agree with experimental NOESY spectrum
Conformers Calculated Total Number	10
Conformers Submitted Total Number	10
Representative Model	1 (fewest violations)

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