Experiment: 1MP7

A Third Complex of Post-Activated Neocarzinostatin Chromophore with DNA. Bulge DNA Binding from the Minor Groove

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	0.9mM complex of NCSi-glu-bulge DNA; 10 mM phophate buffer containing 0.1 mM EDTA, pH 6.0	90% H2O-10% D2O, 100% D2O	10 mM Sodium Phosphate, 0.1 mM EDTA, pH 6.0	6.0	ambient	268
2	2D TOCSY	0.9mM complex of NCSi-glu-bulge DNA; 10 mM phophate buffer containing 0.1 mM EDTA, pH 6.0	90% H2O-10% D2O, 100% D2O	10 mM Sodium Phosphate, 0.1 mM EDTA, pH 6.0	6.0	ambient	268
3	DQF-COSY	0.9mM complex of NCSi-glu-bulge DNA; 10 mM phophate buffer containing 0.1 mM EDTA, pH 6.0	90% H2O-10% D2O, 100% D2O	10 mM Sodium Phosphate, 0.1 mM EDTA, pH 6.0	6.0	ambient	268
4	H-P Cosy, COSY-45, T1 measurement, Translational diffusion constant measurement	0.9mM complex of NCSi-glu-bulge DNA; 10 mM phophate buffer containing 0.1 mM EDTA, pH 6.0	90% H2O-10% D2O, 100% D2O	10 mM Sodium Phosphate, 0.1 mM EDTA, pH 6.0	6.0	ambient	268

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AMX	600
2	Bruker	AMX	600

NMR Refinement
Method	Details	Software
distance geometry, simulated annealing, restrained molecular dynamics	the structure calculation was based on a total of 316 restraints, 258 NOE-derived distance constraints, 40 of dihedral angle restraints, and 18 distance restraints from hydrogen bonds of Wason-Creek base pairs.	UXNMR

NMR Ensemble Information
Conformer Selection Criteria	all calculated structures submitted, back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
Conformers Calculated Total Number	9
Conformers Submitted Total Number	9
Representative Model	1 (closest to the average)

Additional NMR Experimental Information
Details	This structure was determined using standard 2D homonuclear and heteronuclear (1H-31P) techniques. Diffusion constant measurement experiment was used to address the conformation of the complex adopting either homoduplex or self-folded hairpin form.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	UXNMR	Aspect X32	Bruker
2	processing	Felix	98 and 2000	Accelrys
3	structure solution	X-PLOR	3.851	Axel T. Brunger
4	data analysis	MARDIGRAS	3.0	Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar
5	refinement	X-PLOR	3.851	Axel T. Brunger