1HT7

STRUCTURE OF A DNA DUPLEX CONTAINING A BISTRAND ABASIC SITE LESION STAGGERED IN A 5'-ORIENTATION.

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	2mM duplex in 20 mM phosphate buffer, pH 7.6; 50 mM NaCl; 1 mM EDTA.	99.96% D2O	not determined	7.6	ambient	298
2	COSY, COSY45, TOCSY, DQFCOSY, HETCOR	2mM duplex in 20 mM phosphate buffer, pH 7.6; 50 mM NaCl; 1 mM EDTA.	99.96% D2O	not determined	7.6	ambient	298
3	2D NOESY	2mM duplex in 20 mM phosphate buffer, pH 7.6; 50 mM NaCl; 1 mM EDTA.	90% H2O/10% D2O (v/v)	not determined	7.6	ambient	276

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	500
2	Varian	INOVA	600

NMR Refinement
Method	Details	Software
Restrained molecular dynamics	1) Heating stage: from 100 to 500 K in 4ps. Introduction of experimental restraints at the end of this stage. 2) High temperature stage: 80 ps dynamics at 500K 3) Cooling stage: From 500 to 300K in 40ps. 4) Equilibration stage: 140ps dynamics at 300K.	Felix

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	30
Conformers Submitted Total Number	6

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	Felix	98	MSI
2	data analysis	MARDIGRAS	5	Borgia & James
3	refinement	X-PLOR	3.1	A. Brunger
4	data analysis	Insight	95	MSI
5	data analysis	Midas	Plus	UCSF
6	data analysis	Curves	5	Sklenar & Lavery