Experiment: 2KH3

NMR Structure of Aflatoxin Formamidopyrimidine alpha-anomer in duplex DNA

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	1H-1H NOESY	1 mM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE-1, 1 mM THYMIDINE-5'-MONOPHOSPHATE-2, 1 mM 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE-3, 1 mM Aflatoxin B1 Formamidopyrimidine-4, 1 mM 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE-5	100% D2O	0.1 NaCl	8.7	1 atm	280
2	1H-1H COSY	1 mM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE-1, 1 mM THYMIDINE-5'-MONOPHOSPHATE-2, 1 mM 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE-3, 1 mM Aflatoxin B1 Formamidopyrimidine-4, 1 mM 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE-5	100% D2O	0.1 NaCl	8.7	1 atm	280
3	1H-1H NOESY	1 mM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE-6, 1 mM THYMIDINE-5'-MONOPHOSPHATE-7, 1 mM 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE-8, 1 mM Aflatoxin B1 Formamidopyrimidine-9, 1 mM 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE-10	90% H2O/10% D2O	0.1 NaCl	8.7	1 atm	280
4	1H-31P COSY	1 mM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE-1, 1 mM THYMIDINE-5'-MONOPHOSPHATE-2, 1 mM 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE-3, 1 mM Aflatoxin B1 Formamidopyrimidine-4, 1 mM 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE-5	100% D2O	0.1 NaCl	8.7	1 atm	280

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	800
2	Bruker	AVANCE	600

NMR Refinement
Method	Details	Software
simulated annealing, molecular dynamics, simulated annealing and rMD refinement in explicit solvent		Amber

NMR Ensemble Information
Conformer Selection Criteria	back calculated data agree with experimental NOESY spectrum
Conformers Calculated Total Number	9
Conformers Submitted Total Number	9
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber	9	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
2	chemical shift assignment	Sparky		Goddard
3	data analysis	Sparky		Goddard
4	processing	TopSpin		Bruker Biospin
5	restraint generation	MARDIGRAS		Borgias, B.A. & James, T.L.
6	structure validation	CORMA		James T.L.
7	data analysis	Curves		Lavery, R. and Sklenar, H