2K4L

Solution structure of a 2:1C2-(2-naphthyl)pyrrolo[2,1-c][1,4]benzodiazepine (PBD) DNA adduct: molecular basis for unexpectedly high DNA helix stabilization.

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H TOCSY	0.68 mM DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3')	90% H2O/10% D2O	130	6.85	ambient	298
2	2D 1H-1H COSY	0.68 mM DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3')	90% H2O/10% D2O	130	6.85	ambient	298
3	2D 1H-1H NOESY	0.68 mM DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3')	90% H2O/10% D2O	130	6.85	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	500

NMR Refinement
Method	Details	Software
simulated annealing	DISTANCES RESTRAINTS WERE CALCULATED FROM THREE-DIMENSIONAL NOESY PEAK VOLUMES BY COMPARING TO REFERENCE VOLUME OF CYTOSINE (2.45 A BETWEEN H5 AND H6). ALL DISTANCE CONSTRAINTS WERE CLASSIFIED ACCORDING TO CROSSPEAK INTENSITIES AS (S) STRONG (1.80 TO 2.90), (M) MEDIUM (1.80 TO 4.00) AND (W) WEAK (D = 4.0, -2.2/+1.0 ). DISTANCE CONSTRAINS WITH METHYL PROTONS WERE CONSIDERED SEPARATELY (D = 4.0 , -2.2/+1.5 ). THE SIMULATED ANNEALING APPROACH WAS USED TO GENERATE 200 STRUCTURES. THE 10 LOWEST ENERGY STRUCTURES WERE CHOSEN AND THE ROOT MEAN SQUARE DEVIATION VALUES CALCULATED.	X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	200
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	X-PLOR NIH	2.16	Schwieters, Kuszewski, Tjandra and Clore
2	collection	TopSpin	1.3	Bruker Biospin
3	processing	TopSpin	1.3	Bruker Biospin
4	peak picking	AMIX	3.5.5	Bruker Biospin
5	chemical shift assignment	AMIX	3.5.5	Bruker Biospin