1KB1

SOLUTION STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING 6-THIOGUANINE OPPOSITE CYTOSINE

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA	100% D2O	25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA	6.78	ambient	298
2	COSY	2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA	100% D2O	25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA	6.78	ambient	298
3	DQF-COSY	2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA	100% D2O	25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA	6.78	ambient	298
4	COSY45	2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA	100% D2O	25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA	6.78	ambient	298
5	TOCSY	2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA	100% D2O	25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA	6.78	ambient	298
6	HETCO	2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA	100% D2O	25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA	6.78	ambient	298
7	2D NOESY	2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA	10 % D2O, 90 % H2O	25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA	6.78	ambient	276

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

NMR Refinement
Method	Details	Software
RESTRAINED MOLECULAR DYNAMICS SIMULATIONS		Felix

NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number
Conformers Submitted Total Number	1

Additional NMR Experimental Information

Details

THE STRUCTURE WAS DETERMINED USING PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND FURTHER REFINED BY THE FULL- RELAXATION MATRIX BACK CALCULATION METHOD. 15 STRUCTURES EACH WERE DETERMINED FROM A- AND B-FORM DNA STARTING STRUCTURES. FIVE DIFFERENT STARTING TEMPERATURES AND THREE DIFFERENT LENGTHS OF TIME SPENT AT THE HIGH- TEMPERATURE STEP MAKE UP THE 15 STRUCTURES. 25 OF THE 30 TOTAL STRUCTURES CONVERGED TO AN RMSD OF .59A OR LESS. THE AVERAGE OF THESE 25 STRUCTURES WAS CALCULATED AND UTILIZED IN THE FULL RELAXATION MATRIX BACK CALCULATIONS. THE MINIMIZED AVERAGE STRUCTURE FROM THIS LAST STEP IS THE FORM THAT IS DEPOSITED HERE.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	Felix	95 AND 98	BIOSYM TECHNOLOGIES, INC.
2	iterative matrix relaxation	X-PLOR	3.857	BRUNGER
3	refinement	X-PLOR	3.857	BRUNGER