1C2Q

SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC THYMIDINE AND POLARITY REVERSALS

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	0.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH* 6.6, D2O			6.6	AMBIENT	298
2	DQF-COSY	0.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH* 6.6, D2O			6.6	AMBIENT	298
3	31P-1H CORRELATION SPECTROSCOPY	0.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH* 6.6, D2O			6.6	AMBIENT	298
4	2D NOESY	0.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH 6.7, 90% H2O/10% D2O			6.7	AMBIENT	298

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

NMR Refinement
Method	Details	Software
SIMULATED ANNEALING/MOLECULAR DYNAMICS	THE STRUCTURE IS BASED ON A TOTAL OF 405 RESTRAINTS: 268 RANDMARDI DERIVED INTERPROTON DISTANCE RESTRAINTS (NON-EXCHANGEABLE: 246; EXCHANGEABLE: 22); 45 DEOXYRIBOSE ENDOCYCLIC TORSION ANGLE RESTRAINTS DERIVED FROM PSEUDOROTATION ANALYSIS; 45 RIBOSE ENDOCYCLIC TORSION ANGLE RESTRAINTS (BROAD, N-TYPE); 46 WATSON-CRICK DISTANCE AND ANGLE RESTRAINTS. THE FINAL AVERAGE STRUCTURE WAS OBTAINED BY COORDINATE AVERAGING OF THE FINAL ENSEMBLE OF RMD/REM STRUCTURES, FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. ALL STRUCTURE CALCULATIONS WERE PERFORMED USING THE SANDER PROGRAM WITHIN AMBER 4.1, AND THE 1994 ALL ATOM NUCLEIC ACID PARAMETERIZATION. ALL CALCULATIONS WERE CONDUCTED IN VACUO, USING A DISTANCE DEPENDENT DIELECTRIC CONSTANT AND 30 A CUT-OFF FOR NON-BONDED INTERACTIONS.	UXNMR

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

Additional NMR Experimental Information
Details	THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR NMR TECHNIQUES

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	UXNMR	2.1	BRUKER
2	iterative matrix relaxation	MARDIGRAS	3.2	BORGIAS & JAMES, 1989
3	data analysis	CORMA	5.2	BORGIAS & JAMES, 1988
4	data analysis	Sparky	3.33	UCSF
5	refinement	Amber	4.1	PEARLMAN ET AL., 1995
6	data analysis	SPHINX/LINSHA		WIDMER & WUTHRICH, 1987
7	data analysis	Curves	5.1	LAVERY & SKLENAR, 1996
8	structure solution	Amber	4.1	PEARLMAN ET AL., 1995