1BPS

MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	NOESY			76 mM	6.8	1 atm	288
2	ROESY			76 mM	6.8	1 atm	288
3	TOCSY			76 mM	6.8	1 atm	288
4	2D EXCHANGE-ONLY SPECTRA			76 mM	6.8	1 atm	288

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	UNITYPLUS	750
2	Varian	UNITYPLUS	600

NMR Refinement
Method	Details	Software
RELAXATION MATRIX REFINEMENT OF NOE DISTANCE RESTRAINTS AND RESTRAINED MOLECULAR DYNAMICS WITH SIMULATED ANNEALING	THE FOLLOWING RESTRAINTS WERE APPLIED IN THE MOLECULAR DYNAMICS/ENERGY MINIMIZATION CALCULATIONS: (1) INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM RELAXATION MATRIX ANALYSIS OF NOE DATA; (2) IMINO PROTON HYDROGEN BOND RESTRAINTS FOR ALL BASE PAIRS EXCEPT THE CENTRAL DA-DG MISMATCH PAIR. THE MODIFIED DA RESIDUE OF THIS MINOR CONFORMER DISPLAYED A C2'-ENDO SUGAR PUCKER AND AN ANTI GLYCOSIDIC BOND. IT FORMED AN ANTI:ANTI BASE PAIR CONTAINING TWO HYDROGEN BONDS WITH THE OPPOSITE DG. THE MODIFIED DA RESIDUE OF THE MAJOR CONFORMER OF THIS MOLECULE [YEH ET AL. (1995) BIOCHEMISTRY 34, 13570-13581] DISPLAYED C3'-ENDO SUGAR PUCKER AND A SYN GLYCOSIDIC BOND. THE MAJOR CONFORMER MODIFIED DA RESIDUE FORMED A SYN:ANTI BASE PAIR CONTAINING NON-WATSON CRICK HYDROGEN BONDS WITH THE OPPOSITE DG. MORE REFINEMENT DETAILS CAN BE FOUND IN THE PRIMARY JOURNAL CITATION (SCHWARTZ ET AL.,1997).	Amber

NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number	1
Conformers Submitted Total Number	1
Representative Model	1 (minimized average structure)

Additional NMR Experimental Information
Details	MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED USING DISTANCE RESTRAINTS DERIVED FROM 2D NOESY EXPERIMENTS DONE IN 99.999% D2O AND 90% H2O/ 10% D2O. 2D ROESY, TOCSY, AND EXCHANGE-ONLY EXPERIMENTS WERE USED IN THE CHEMICAL SHIFT ASSIGNMENT PROCESS.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber	4.1	PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN
2	structure calculation	MORASS	2.2	Luxon
3	structure calculation	Amber	4.1	PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.